option not to print warning messages (eg re overlapping mates)

biod / sambamba

Tools for working with SAM/BAM data

http://thebird.nl/blog/D_Dragon.html

GNU General Public License v2.0

557 stars 104 forks source link

option not to print warning messages (eg re overlapping mates) #452

Closed aledj2 closed 3 years ago

aledj2 commented 4 years ago

When running with -m warning messages (mates overlap in index are fixed/detected) are printed to stderr. These messages slow down execution. Redirecting 2>/dev/null would lose any other error messages

I'm using v0.7.1 static binary

aledj2 commented 4 years ago

Realised I didn't state this is with depth

As the warning message can't be traced to a single read, perhaps a count can be reported at the end, eg

x mates fixed y mates detected

I've looked to see if I can suggest a patch but I'm not at all familiar with d (sorry)

pjotrp commented 3 years ago

No activity

Sven-Winter commented 1 year ago

What a pity that there was no response. I receive "mates overlap in index" warnings, and it produces giant log files for no reason.