maf-convert: no PG line
Hello,
First, this is a minor thing. Still, it may be useful to include in the SAM header at least some info about the lastal version/command line options used for mapping fastq reads. In the SAM/BAM world often programs add an extra line to the header, so to some extent even an oldish BAM file is semi-documented. No idea if adding to MAF header I guess at the lastal stage something like:
# @PG ID:lastal PN:lastal VN:1296 CL:lastal -v -P4 -Q1 -C2 -p train_out hg38.lastdb my_input.fq.gz
and then fishing it out in maf-convert so it will end up in SAM makes sense to others.
Hope it helps.
Darek Kedra