mmokrejs
commented
6 years ago Old samtools-0.1.x series doe snot understand --version:
$ samtools --version
[main] unrecognized command '--version'
$ samtools sort
Usage: samtools sort [options] <in.bam> <out.prefix>
Options: -n sort by read name
-f use <out.prefix> as full file name instead of prefix
-o final output to stdout
-l INT compression level, from 0 to 9 [-1]
-@ INT number of sorting and compression threads [1]
-m INT max memory per thread; suffix K/M/G recognized [768M]Newer samtools:
$ samtools --version
samtools 1.5
Using htslib 1.5
Copyright (C) 2017 Genome Research Ltd.
$ samtools sort
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
-o FILE Write final output to FILE rather than standard output
...The patch should test for version of samtools to decide which syntax to use. However, I think the patch is nevertheless wrong. Either you want to use shell redirect or you use -o $outfilename.
A-Tsai
In my environment, I use apt to install samtools and get the help description of samtools sort as follows:
test@sga1:/home/test/sga$ samtools sort Usage: samtools sort [options]
Options: -n sort by read name
-f use as full file name instead of prefix
-o final output to stdout
-l INT compression level, from 0 to 9 [-1]
-@ INT number of sorting and compression threads [1]
-m INT max memory per thread; suffix K/M/G recognized [768M]
the parameter -o of samtools sort is for stdout rather than for user-defined output filename. It will cause failure when calling sga-bam2de.pl. Since many version of samtool are available in the world, it will be better to simplify the general usage of samtools.