Parseable output format (-m 10): wrong scores printed for subsequent hit

[flange-ipb]

Hello,

in case a library sequence produces more than one alignment hit, the scoring printed for the subsequent hit (alignment starts with ">--") is the one of the first hit, which is incorrect. I observe this for output format 10, but not for the standard format 0.

Files for reproduction: library and query

Result examples: output format 10: compare lines 116-118 (first hit) with lines 150-152 (second hit, incorrect scores) output format 0: compare line 61 (first hit) with line 77 (second hit, correct scores)

Best regards, Frank

[wrpearson]

Frank --

I have found and fixed the problem, and hopefully will be able to upload the changes to GitHub in the next day or so (unfortunately I will have much less internet connectivity for the next month).

Here is the required change:

diff --git a/src/mshowalign2.c b/src/mshowalign2.c index 513424f..1e5b20a 100644 --- a/src/mshowalign2.c +++ b/src/mshowalign2.c @@ -748,9 +748,9 @@ void showalign (FILE *fp, unsigned char *aa0, unsigned char aa1save, int maxn, if (info_str[0]) fprintf(fp,"; %s_info: %s\n",m_msp->f_id0,info_str); if (ppst->zsflag>=0) fprintf (fp,"; %s_z-score: %4.1f\n; %s_bits: %3.1f\n; %s_expect: %6.2g\n",

• m_msp->f_id0,bbp->zscore,
• m_msp->f_id0,zs_to_bit(bbp->zscore, m_msp->n0, bbp->seq->n1),
• m_msp->f_id0,bbp->rst.escore);
• m_msp->f_id0,lzscore,
• m_msp->f_id0,zs_to_bit(lzscore, m_msp->n0, bbp->seq->n1),
• m_msp->f_id0,zs_to_E(lzscore, bbp->seq->n1, ppst->dnaseq, ppst->zdb_size, m_msp->db));

  else

  if ((m_msp->markx & MX_M11OUT) == 0) {
    fprintf (fp,"; %s_%s: %d\n", m_msp->f_id0, m_msp->alab[0], lsw_score);

Bill Pearson

[flange-ipb]

Hello Bill,

excellent! This patch solves the issue.

Thanks for your quick support! Frank

[wrpearson]

Corrected in latest v36.3.8 version