

============ projects/tests/file/test_file.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          4

--------         END              --------




============ projects/tests/blast/test_blast_parsing.h ============

-------- General File Information --------

 
 uses some custom IO, test will have to be adapted anyways
 


--------      Statistics         --------

 # of tagged functions, structs etc:                12
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/tests/graph_algorithms/test_graph_algorithms.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/pipe/pool_base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           4

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          4

--------         END              --------




============ projects/library/seqan/seeds2/seeds_seed_simple.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/seeds2/seeds_seed_set_base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/seeds2/seeds_seed_chained.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/seeds2/align_chain_banded.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/chaining/chain_wrapper_point.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           4

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_msa/graph_align_tcoffee_refinement.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_msa/graph_align_tcoffee_io.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                12
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    12

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          12

--------         END              --------




============ projects/library/seqan/align/align_hirschberg.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/align/gaps_base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    2

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/align/align_base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/align/align_myers.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/refinement/graph_impl_align_adapt.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           3

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          3

--------         END              --------




============ projects/library/seqan/refinement/graph_impl_align.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                6
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    4

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          4

--------         END              --------




============ projects/library/seqan/system/system_thread.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           2

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/system/file_sync.h ============

-------- General File Information --------

 
 
 contains third way of file-io, low level platform specific, i.e. fd for
 POSIX and handles for WINDOWS
 
 not clear in which places this is used exactly
 
 SEQAN_DIRECTIO used on UNIX, not sure exactly what it does
 use of other macros unclear aswell
 


--------      Statistics         --------

 # of tagged functions, structs etc:                13
 # falsely tagged (regex false positive):           0

 # well documented:                                 1
 # not documented but should be:                    5

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/system/system_manual_forwards.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/system/file_directory.h ============

-------- General File Information --------

 
 contains windows specific code
 
 
 used by file/file_format_mmap.h and some apps
 no documentation at all
 


--------      Statistics         --------

 # of tagged functions, structs etc:                17
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    17

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/system/file_async.h ============

-------- General File Information --------

 
 
 contains third way of file-io, low level platform specific, i.e. fd for
 POSIX and handles for WINDOWS
 
 not clear in which places this is used exactly
 
 SEQAN_DIRECTIO used on UNIX, not sure exactly what it does
 use of other macros unclear aswell
 
 not sure about all the AsyncRequest stuff, as most related calls are
 deactivated in code, see also file/file_base.h
 


--------      Statistics         --------

 # of tagged functions, structs etc:                31
 # falsely tagged (regex false positive):           0

 # well documented:                                 18
 # not documented but should be:                    9

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/blast/blast_hsp.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    2

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/blast/blast_stream_hsp_iterator.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/blast/blast_parsing.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/blast/blast_stream_report.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/blast/blast_hit.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/blast/blast_report.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    3

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/blast/blast_stream_hit.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/blast/blast_stream_hit_iterator.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/score/score_matrix.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                8
 # falsely tagged (regex false positive):           2

 # well documented:                                 0
 # not documented but should be:                    6

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          7

--------         END              --------




============ projects/library/seqan/store/store_contig.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/store/store_io_ucsc.h ============

-------- General File Information --------

 
 
 
 maybe move this to file/ because its a file format
 


--------      Statistics         --------

 # of tagged functions, structs etc:                6
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    2

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/store/store_io_bam.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                5
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             1

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          3

--------         END              --------




============ projects/library/seqan/store/store_io_sam.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                14
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    7

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             1

 # that contain an obvious bug:                     1
 # that duplicate existing functionality:           2
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          11

--------         END              --------




============ projects/library/seqan/store/store_io_gff.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                11
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    10

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           1
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/store/store_io.h ============

-------- General File Information --------

 
 
 
 if this file is about the amos file format why isn't it named accordingly?
 
 altogether it is unclear why sequence io is in file/ but store io is in
 store/
 


--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           0

 # well documented:                                 1
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/graph_align/graph_align_smith_waterman.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           2

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/statistics/statistics_markov_model.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/basic/basic_profile.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                21
 # falsely tagged (regex false positive):           17

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          6

--------         END              --------




============ projects/library/seqan/basic/basic_debug.h ============

-------- General File Information --------

 
 contains a TODO by holtgrew indicating that this should be merged into
 basic_testing.h
 
 these functions use custom IO, i.e. FILE* fopen etc
 might be ok for binary comparison
 
 not sure what the text-comparison is all about. If you want to compare
 text, ignoring differences in EOL-style, you should not use binary
 file reading at all, but text-mode reading which converts line-endings
 on the fly anyhow, rendering this code useless (IMHO)
 
 code contains goto statements which could easily be replaced by clean code
 (I didn't even know this is possible in c++


--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          3

--------         END              --------




============ projects/library/seqan/basic/basic_profchar.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           2

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/basic/basic_testing.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           1
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/consensus/consensus_score.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           3

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/consensus/consensus_base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    4

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/graph_algorithms/graph_algorithm.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/misc/misc_parsing.h ============

-------- General File Information --------

 
 
 
 used in different places
 except one function non are documented
 
 NOTE atof is used in some functions, but according to standard this is
 locale dependent (',' or '.' as decimal seperator). Has someone experienced
 issues with this? we should probably replace it with a local independent
 version to make sure
 
 Also in general atof should be replaced with strod, atoi with strtol etc
 
 it should also be noted that there are standard C functions in ctype.h
 for the _is* cases, e.g. isspace(), isdigit() isprint(), isalnum() etc
 why don't we use these?
 
 when returning a string we should remember to always use Generous() as
 resize policy to avoid some reallocation efforts (some parsing functions
 do this already, others don't)
 


--------      Statistics         --------

 # of tagged functions, structs etc:                29
 # falsely tagged (regex false positive):           0

 # well documented:                                 1
 # not documented but should be:                    28

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     3
 # that duplicate existing functionality:           5
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          29

--------         END              --------




============ projects/library/seqan/misc/misc_cmdparser.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                7
 # falsely tagged (regex false positive):           2

 # well documented:                                 0
 # not documented but should be:                    5

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          7

--------         END              --------




============ projects/library/seqan/misc/misc_svg.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/graph_types/graph_impl_directed.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_types/graph_impl_undirected.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_types/graph_impl_automaton.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_types/graph_utility_parsing.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/graph_types/graph_drawing.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                17
 # falsely tagged (regex false positive):           0

 # well documented:                                 3
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/graph_types/graph_impl_hmm.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_types/graph_impl_tree.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/graph_types/graph_impl_wordgraph.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/sequence/sequence_stream.h ============

-------- General File Information --------

 
 seems to be an interface that provides _stream operations on anything
 iterable, would have to be adapted to new interface and could be moved
 to io-module.
 
 does not use C-References, therefore current interface is NOT compatible


--------      Statistics         --------

 # of tagged functions, structs etc:                10
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/find_motif/profile.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           3

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/index/index_esa_drawing.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/index/index_wotd.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           4

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/index/index_esa_stree.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                4
 # falsely tagged (regex false positive):           4

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/index/index_base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/find/find_horspool.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/find/find_wild_shiftand.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/file/file_format_cgviz.h ============

-------- General File Information --------

 
 tested in tests/file/test_file.h
 tag mentionen in doc, but no further documentation, no link to spec
 


--------      Statistics         --------

 # of tagged functions, structs etc:                8
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          3

--------         END              --------




============ projects/library/seqan/file/file_format_raw.h ============

-------- General File Information --------

 
 
 has some documentation, but could be better
 apperently tested by tests/file/test_file.h, used in some other places
 
 unclear why static members are used and functions not overloaded directly
 
 raw is defined as default behaviour for read and write, is this desired
 or should read and write maybe auto-detect fileformat?
 


--------      Statistics         --------

 # of tagged functions, structs etc:                17
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/file/cstream.h ============

-------- General File Information --------

 
 
 Tested by tests/file
 documentation non-existent
 relation to file_cstyle.h not clear
 Metafunctions supposedly moved to file_cstyle.h are commented there too


--------      Statistics         --------

 # of tagged functions, structs etc:                17
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           9
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          11

--------         END              --------




============ projects/library/seqan/file/file_array.h ============

-------- General File Information --------

 
 
 Basically contains stuff fro striped and Chained file access
 (a little) documentation for both is in file_base
 Chained-tag has no test-case but is used in different demos
 Striped-tag has no test-case and AFAICT is not used in any app
 functions used are those of file_cstyle.h not cstream.h
 not clear why certain things are here and other in file_base
 
 I am unsure whether Striped works at all, there seems to be no open
 functions or other functions for acutally assigning multiple files
 to the Striped virtual file


--------      Statistics         --------

 # of tagged functions, structs etc:                36
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             1

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/file/string_external.h ============

-------- General File Information --------

 
 
 mostly documented (doc for some functions missing)
 not tested in any test case nor used in any app right now
 -> needs testing, especially different iterators


--------      Statistics         --------

 # of tagged functions, structs etc:                99
 # falsely tagged (regex false positive):           0

 # well documented:                                 7
 # not documented but should be:                    9

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     1
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          8

--------         END              --------




============ projects/library/seqan/file/file_page_raid0.h ============

-------- General File Information --------

 
 not tested by any test or app
 no documentation for the functions
 
 hard to say how/if this works, since there is no doc
 


--------      Statistics         --------

 # of tagged functions, structs etc:                7
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    7

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/file/file_format.h ============

-------- General File Information --------

 
 
 well documented
 apperently tested by tests/file/test_file.h
 
 
 AFAICT this not really used widely, as the FileFormat specialization
 tags are used diretly e.g.
      read(TFile, TData, TMeta, Fasta)
 and not
      read(TFile, TData, TMeta, FileFormat<TFile, TData, TMeta, Fasta>)
 
 the global wrappers in this file also break down to this behaviours
 
 however it is not evident what the purpose of the FileFormat class is
 altogether and especially the virtual members
 (except being return value for guessFileFormat, which could aswell return
 the tag)
 
 -----------------
 
 contains all sorts of stream-IO helper functions that should go someplace
 else.
 
 For all of these: Should we really look at c passed as argument, how do
 we know, c is actually current character?
 
 For the iterators the current mechanism is error-prone:
 
 foobar (TInput & input, TIterator it)
 {
     Iterator<TInput, Standard()> it_end = end(input);
     while (it != it_end)
          ...
 
 }
 
 this does not guarantee, that it and it_end are the same type, since
 it maybe non-standard
 
 also some functions set it_end = end(input) - 1; which seems to be related
 to change of atEnd behaviour http://trac.mi.fu-berlin.de/seqan/wiki/IoRevision
 
 IMO all these functions should be changed to not construct a 2nd iterator
 but use atEnd() directly
      


--------      Statistics         --------

 # of tagged functions, structs etc:                26
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    10

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     3
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          10

--------         END              --------




============ projects/library/seqan/file/stream_algorithms.h ============

-------- General File Information --------

 
 
 mostly documented (doc for some functions missing)
 used ubiquitously, but possibly not all specializations
 
 functions seem to be agnostic of FileType (stream.h or cstream.)
 it is not clear if both are actually tested (but shouldn't matter
 if underlying routines work correctly)


--------      Statistics         --------

 # of tagged functions, structs etc:                11
 # falsely tagged (regex false positive):           0

 # well documented:                                 6
 # not documented but should be:                    5

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/file/file_base.h ============

-------- General File Information --------

 
 base class with SPecs and Tags
 also contains standard calls for IO as wrappers around members
 in system/file_sync.h and system/file_ssync.h
 (hese files are built around c++ fstream IO)
 well documented (in comparison to other files)
 
 SEQAN_DIRECTIO Macro mentioned here but not documented or tested


--------      Statistics         --------

 # of tagged functions, structs etc:                38
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    2

 # that don't do anything, but maybe should:        6
 # that seem to be incomplete/not done:             4

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           1
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          18

--------         END              --------




============ projects/library/seqan/file/file_cstyle.h ============

-------- General File Information --------

 
 
 Tested by tests/file
 documentation non-existent
 relation to cstream.h not clear
 Metafunctions supposedly moved hereto from file_cstyle.h are commented here awell


--------      Statistics         --------

 # of tagged functions, structs etc:                19
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           7
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          11

--------         END              --------




============ projects/library/seqan/file/file_format_guess.h ============

-------- General File Information --------

 
 only works if seeking is possible
 
 the whole FileFormat class seems useless, see file_format.h
 this could aswell return the specific tag
 
 description in code comments not plausible


--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 1
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/file/file_forwards.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/file/string_mmap.h ============

-------- General File Information --------

 contains windows specific code
 
 
 tested in library/demos/howto/efficiently_import_sequences.cpp and stellar
 
 relation to file_format_mmap.h unclear
 
 relation to string_external unclear, what benifit does string_mmap provide?
 
 contains windows-specific code


--------      Statistics         --------

 # of tagged functions, structs etc:                46
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    11

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          5

--------         END              --------




============ projects/library/seqan/file/stream.h ============

-------- General File Information --------

 
 well documented
 tested by tests/file and probably used by a lot of stuff
 c++ equivalent to  cstream.h


--------      Statistics         --------

 # of tagged functions, structs etc:                40
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/seqan/file/file_format_mmap.h ============

-------- General File Information --------

 
 
 mostly documented
 contents seems to be used widely in apps
 
 contains all sorts of private _is* and _stream* functions
 
 contains many file format specific functions and even two new file format
 definitions (fastq and qsec) that should definitely go someplace else,
 
 contains almost nothing specific to MemoryMapped strings, other than
 the split()-calls


--------      Statistics         --------

 # of tagged functions, structs etc:                68
 # falsely tagged (regex false positive):           0

 # well documented:                                 47
 # not documented but should be:                    13

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             1

 # that contain an obvious bug:                     2
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           1

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          25

--------         END              --------




============ projects/library/seqan/file/file_filereaderiterator.h ============

-------- General File Information --------

 
 
 relation to file_filereader.h not totally clear
 
 broken according to holtgrew, but used by many file_format implementations
 that supposedly work
 
 not yet fully understood how this works or is supposed to
 
 


--------      Statistics         --------

 # of tagged functions, structs etc:                9
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/file/file_format_fasta_align.h ============

-------- General File Information --------

 
 tested in tests/file/test_file.h
 tag mentionen in doc, but no further documentation, no link to spec
 
 
 bacthreading and -writing
 
 does not treat IDs as Meta-Data, while format_fasta does
 


--------      Statistics         --------

 # of tagged functions, structs etc:                14
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     1
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          3

--------         END              --------




============ projects/library/seqan/file/file_filereader.h ============

-------- General File Information --------

 
 
 Tested by tests/file and various demos, but only the fasta-specialization
 basic documentation
 uses cstream.h's functions
 Metafunctions supposedly moved hereto from file_cstyle.h are commented here awell
 
 not fully understood how this works and what relation of the iterators is
 
 possibly broken according to holtgrew
 


--------      Statistics         --------

 # of tagged functions, structs etc:                64
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/seqan/file/chunk_collector.h ============

-------- General File Information --------

 
 this class is only used file_format_raw
 it is tested by test_file which tests file_format_raw
 it is sparsely documented, but marked as Internal anyway (does it need doku
 then?)
 TODO not fully understood implications of assign and replace


--------      Statistics         --------

 # of tagged functions, structs etc:                32
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/seqan/file/file_page.h ============

-------- General File Information --------

 
 not tested by any test or app
 no documentation for the functions
 
 contains lots of seemingly important code, however doc is sparse
 to non-existent. Code needs thorough investigation, to understand
 how/if this works
 
 probabyl Weese's code according to holtgrew
 
 


--------      Statistics         --------

 # of tagged functions, structs etc:                76
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    30

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          5

--------         END              --------




============ projects/library/seqan/file/file_format_genbank.h ============

-------- General File Information --------

 
 tested in tests/file/test_file.h
 tag mentionen in doc, but no further documentation, no link to spec
 
 current spec:
 ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
 
 IMPORTANT: from what I understand: fileReaderIterator does not iterate
 through records, but through lines of the sequence of one record.
 goNext() on the iterator goes to beginning of next line and sets
 data boundaries for next iteration
 
 goNext() on the file itself goes to the beginning of the next record.
 
 THIS is not intuitive AT ALL.


--------      Statistics         --------

 # of tagged functions, structs etc:                11
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          7

--------         END              --------




============ projects/library/seqan/file/file_format_embl.h ============

-------- General File Information --------

 
 tested in tests/file/test_file.h
 tag mentioned in doc, but no further documentation, no link to spec
 
 should be broken, because based on filereaderiterator which is broken
 according to holtgrew.
 
 IMPORTANT: from what I understand: fileReaderIterator does not iterate
 through records, but through lines of the sequence of one record.
 goNext() on the iterator goes to beginning of next line and sets
 data boundaries for next iteration
 
 goNext() on the file itself goes to the beginning of the next record.
 


--------      Statistics         --------

 # of tagged functions, structs etc:                14
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     1
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          5

--------         END              --------




============ projects/library/seqan/file/file_format_fasta.h ============

-------- General File Information --------

 
 tested in tests/file/test_file.h
 tag mentionen in doc, but no further documentation, no link to spec
 
 IMPORTANT: from what I understand: fileReaderIterator does not iterate
 through records, but through lines of the sequence of one record.
 goNext() on the iterator goes to beginning of next line and sets
 data boundaries for next iteration
 
 goNext() on the file itself goes to the beginning of the next record.


--------      Statistics         --------

 # of tagged functions, structs etc:                18
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    4

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          10

--------         END              --------




============ projects/library/seqan/find2/find_pattern_wild_shiftand.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           1
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/indel_simulator/indel_simulator.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                5
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           4
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          5

--------         END              --------




============ projects/library/apps/micro_razers/micro_razers.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/seqcons/seqcons.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/stellar/stellar.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                5
 # falsely tagged (regex false positive):           5

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/stellar/stellar_extension.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/stellar/stellar_types.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/stellar/stellar_output.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             1

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/snp_store/snp_store.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/insegt/read_gtf.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/insegt/base.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           2
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/apps/insegt/read_gff.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/tree_recon/tree_recon.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/razers/paramChooser.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                7
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           1
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          5

--------         END              --------




============ projects/library/apps/razers/razers.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/razers2/razers.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/razers2/paramChooser.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                7
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           1
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          5

--------         END              --------




============ projects/library/apps/rep_sep/utils.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                3
 # falsely tagged (regex false positive):           2

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           1

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/rabema/intervals.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                5
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    1

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          3

--------         END              --------




============ projects/library/apps/rabema/wit_store.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/apps/splazers/splazers.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/splazers/paramChooser.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                7
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          7

--------         END              --------




============ projects/library/apps/mason/mason.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/mason/util.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          2

--------         END              --------




============ projects/library/apps/prob_spec/stellar_types.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/prob_spec/stellar_extension.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                1
 # falsely tagged (regex false positive):           1

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------




============ projects/library/apps/prob_spec/stellar_output.h ============



--------      Statistics         --------

 # of tagged functions, structs etc:                2
 # falsely tagged (regex false positive):           0

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          1

--------         END              --------




============ projects/library/apps/prob_spec/probspec.cpp ============



--------      Statistics         --------

 # of tagged functions, structs etc:                5
 # falsely tagged (regex false positive):           5

 # well documented:                                 0
 # not documented but should be:                    0

 # that don't do anything, but maybe should:        0
 # that seem to be incomplete/not done:             0

 # that contain an obvious bug:                     0
 # that duplicate existing functionality:           0
 # that can be removed for other reasons:           0

 # of parsing functions that get "TChar c&":        0

 # with free-text comment:                          0

--------         END              --------


