samtools/samtools — pull request #114 by pruzanov (2014-01-22 19:16:02+00:00)
Title: blast2sam.pl fixed, tested with ncbi-blast-2.2.29+, samtools 0.1.19 and picard 1.72

Fixed a few bugs:
1. CIGAR string was reporting insertions instead of deletions (and the other way around)
2. the script was adding a line with erroneous data at the end of the .sam file even if the last entry was not properly mapped in blast output (added a check)
3. Added dummy score generation/printing so that the base score field (sam field #11) could have something (this was causing some problems, too) This is controlled with option -d now
4. Added POD