Open kiwiroy opened 7 years ago
Thanks will try out shortly
Works as expected writing to named file..Many thanks
[05:03][cfljam@aklppf31:npstat (output-filename)] $ git branch -v
master ef389e8 Add files via upload
* output-filename 7d3cf0f add an output file option `-stats`
[05:03][cfljam@aklppf31:npstat (output-filename)] $ ./npstat
no pileup file supplied
Missing values in command line!
Command:
npstat [options] file.pileup
or to read from standard input:
npstat [options] -
Options:
-n samplesize : haploid sample size
-l windowlength : window length
-mincov minimum_coverage : filter on minimum coverage (default 4)
-maxcov maximum_coverage : filter on maximum coverage (default 100)
-minqual minimum_base_quality : filter on base quality (default 10)
-nolowfreq m : filter on minimum allele count mac>m
-outgroup file.fa : outgroup file in FASTA
-annot file.gff3 : annotation file in GFF3
-snpfile file.snp : consider SNPs only if present in file.snp
-stats file.stats : output stats to an alternately named file
As an option for #3.
As
npstat
outputs progress status to stdout the following might be an option @cfljam.gzip -dc pileup.gz | npstat [options] -stats >(cat) - >/dev/null