Typo in samtools sort command bowtie2 manual page

[ambi1999]

Hi,

A very minor type in samtools sort command on the following bowtie2 manual page. Basically -o output has not been added.

Page http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

Present command: samtools sort eg2.bam eg2.sorted

Correct command: samtools sort eg2.bam -o eg2.sorted

ps: I know this is very minor issue but just thought to mention incase it helps someone.

Cheers,
Ambi.

[BenLangmead]

Agree that this should be fixed. The usage in the manual does work for older versions of samtools. I think it should work for all versions < 1.0. But for more recent versions, this command should be:

 samtools sort eg2.bam -o eg2.sorted.bam

(note the .bam at the end of the output file, since we're specifying the full filename rather than just the prefix, as we did in samtools versions <1.0)

The bcftools command in the manual may also need to be updated. I got invalid option -- b when I tried it just now. Not sure what changed there.

[dnbh]

Using a positional argument in place of -o was also still supported under the "legacy" options without last I checked, though that was in the 1.2 series.