sambamba validate does not produce output

biod / sambamba

Tools for working with SAM/BAM data

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

GNU General Public License v2.0

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sambamba validate does not produce output #430

Closed elcortegano closed 4 years ago

elcortegano commented 4 years ago

I am running sambamba validate file.bam with some BAM files, but this does not produce any output. Only:

sambamba 0.7.1
 by Artem Tarasov and Pjotr Prins (C) 2012-2019
    LDC 1.17.0 / DMD v2.087.1 / LLVM8.0.1 / bootstrap LDC - the LLVM D compiler (1.17.0)

This is happening for files both with errors and without them (validated with picard).

Am I running this in a wrong way? Other tools as markdup seem to run fine.

pjotrp commented 4 years ago

If you read the source code you should be able to figure out what validate does.