jaudoux/counttags

countTags is a c++ optimized software that counts occurrences of a set of k-mer signatures into a set of FASTQ (possibly gziped) files.

counttags's Issues

option -k and -t

Options -k and -t are not correctly writing with --help:

countTags --help
countTags
USAGE: countTags [options] tags.fa seq.fastq[.gz]

Options:
  --help          Print usage and exit.
  -k=INT          tags length
  -m=INT          max number of reads
  -t=INT          number of threads
  --stranded      strand-specific protocol
  --normalize     normalize counts
  --tag-names     print tag names in the output
  --merge-counts  merge counts from all input FASTQs

-k=32 doesn't works but -k 32, -k32 and --k=32 seems ok.
It is the same issue whith -t option, but multithreading doesn't works for me (should be removes this option ?)