sambamba merge with stdout not working

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 merge with stdout not working #435

Closed nh13 closed 4 years ago

nh13 commented 4 years ago

sambamba merge /dev/stdout 1.bam 2.bam > out.bam does not work on 0.6.6 and 0.7.1 installed via bioconda on OSX. It looks like I omit the > out.bam pipe, I get the BAM file printed to stdout (crazy characters to the terminal). Any ideas?

pjotrp commented 4 years ago

The crazy characters are the BAM output. Try outputting SAM instead.