# Bugs found 4/2/03

The following command line yields a bug:

  mhmm -verbose 1 -meme input/crp0.meme.html -noheader -noparams -type complete  

In the resulting output, line 584 contains the reverse complement of
the corresponding line (723) from the input file input/crp0.meme.html.
This is apparently the only state in which this problem occurs.

Here is a simpler command line that yields the same bug:

  meme-io -verbose 1 -meme input/crp0.meme.html 

Here, the problem is in line 77.

I have compiled the code on different dates and narrowed down the date
when it was introduced.  The bug does not appear on 2003/01/01, but it
does appear on 2003/01/15.  Between those two dates, the following
files changed:

P cmdline.h
P fitevd.c
P fitevd.h
P gendb.c
P gendb.h
P match.c
P mhmms.c
P mhmms.h
P mhmmscan.c
P motif.c
P pssm.c
P seq.c
P seq.h

cvs diff -r 1.22 -r 1.21 motif.c
Index: motif.c
===================================================================
RCS file: /projects/science/cvs-repository/mhmm/base/src/motif.c,v
retrieving revision 1.22
retrieving revision 1.21
diff -r1.22 -r1.21
158c158
<   for (i = 0; i < (int)((a_motif->length + 1) / 2); i++) {
---
>   for (i = 0; i < (int)(ceil(a_motif->length / 2)); i++) {
