Option to output bamUtil stats to STDOUT rather than to a file

[dylkot]

Hi There,

I am using bamUtil stats to analyze some whole-genome sequencing data like so

curl url_for_my_large_bam.bam | ./bam stats --in -.ubam --cBaseQC results.txt

and results.txt is really large. I would love to be able to pipe it to awk to do some filtering. It seems like it would be pretty easy to add an option to write to STDOUT. Is this an option I am missing or would it be possible to add?

Thanks, Dylan

[pjvandehaar]

curl url_for_my_large_bam.bam | ./bam stats --in -.ubam --cBaseQC -

works for me. I just added - to bam stats --help in the commit https://github.com/statgen/bamUtil/commit/eb542172119d0f2b43ede03f24163f88e3478340 .

In general, any time that you want to pipe something to stdout using a filename, you can use /dev/fd/1. Example:

curl url_for_my_large_bam.bam | ./bam stats --in -.ubam --cBaseQC /dev/fd/1 2>/dev/null | cut -f1 | uniq -c

(The 2>/dev/null discards the line Number of records read = 10000.)

[dylkot]

HI pjvandehaar, thank you for the tip! I will use that.