Psl2sam Pl

# 2) Use custom score weights for matches, mismatches, gap opens, and extensions
psl2sam.pl \
  -a 2 -b 4 -q 5 -r 1 \
  alignments.psl > rescored.sam

# 3) Stream PSL from stdin
cat alignments.psl | psl2sam.pl > alignments.sam

Recommended Workflow

1. Confirm the input is ordinary PSL and not PSLX or some downstream PSL-derived report.
2. Decide whether the default score weights are acceptable or whether you need explicit -a, -b, -q, and -r values.
3. Convert to SAM, then inspect a few long-gap records to confirm the CIGAR output is acceptable for your downstream use.
4. If the PSL represents spliced transcript alignments, verify whether this simple converter is sufficient before using the result in splice-aware analyses.

Guardrails

• -a, -b, -q, and -r only change the computed AS:i score; they do not alter the underlying alignment coordinates.
• The script does not emit reference-skip N operators in CIGAR strings, so intron-like PSL gaps are represented as insertions/deletions instead of splice skips.
• Help comes from Perl Getopt::Std, so --help works generically but -help is the wrong pattern for this script family.
• Output is plain SAM records without a SAM header.