Chromosome names with more than two characters

[lczech]

Just a quick observation and question: If I am reading the input fasta parsing correctly

PoolSNP/PoolSNP.sh

Line 207 in 0197a5c

grep '^>' $ref | awk '$1!~/\|/ && $1!~/\// && $1!~/\\/ && $1!~/,/' | awk -v inp="$out" -v cut="$mac" -v script_dir="$SCRIPTS_DIR" '{print "python3 " script_dir "/max-cov.py --mpileup " inp "/temp/cov/mpileups/" substr($1,2) ".mpileup.gz --cutoff " cut " --contig " substr($1,2) " --out " inp "/temp/cov/cutoffs/" substr($1,2) ".txt"}' > $out/temp/contignames.txt

you are using substr($1,2) to get the contig names, right? So, does that mean that PoolSNP only works if all chromosome names are exactly two characters long? That might work for Drosophila, but certainly not for many other species. Or am I misunderstanding what is happening there?

Cheers and so long
Lucas