[notbug] unexpected termination on fasta.gz

[korziner]

Unexpected termination returns

2 �
9590 >

by the command:

~/miniconda3/bin/bioawk '/^>/ {count[substr($0,1,1)]++}END{for(j in count) print count[j],j}' SILVA_128_SSURef_tax_silva_full_align_trunc.fasta.gz

Reference gzip and mawk commands (doing the same count) are OK:

time zcat *fasta.gz|./bioawk '/^>/ {count[substr($0,1,1)]++}END{for(j in count) print count[j],j}'
1922213 >

real	47m44.564s
user	46m22.997s
sys	2m48.813s

time zcat *fasta.gz|mawk '/^>/ {count[substr($0,1,1)]++}END{for(j in count) print count[j],j}'
1922213 >

real	10m47.346s
user	11m31.835s
sys	1m44.985s

Is it similar to zgrep, which can search both in compressed and not compressed, or -c fastx should be explicit?

[lh3]

bioawk usually doesn't read gzip'd files. It only works with gzip'd files when you use "-c".

[korziner]

OK, notbug, just misuse