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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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Does `-bam -` send the BAM to stdout ? #52

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

I was trying to send -bam to stdout using /dev/stdout but it failed, but - worked which was good.

I could not find any documentation for this feature.

Does it work for -output_vcf and -sam too?

hsinnan75 commented 4 years ago

MapCaller checks the output filename in case the output file cannot be created. Unfortunately, /dev/stdout and /dev/stderr are not accepted. I'll fix this problem.

tseemann commented 4 years ago

If - works (which it does?), then nothing needs to be done. - is a common practice in Unix for stdin.

Just add documentation about it :-)

hsinnan75 commented 4 years ago

Hi, I've fixed the problem. Now MapCaller can output to /dev/stdout.

tseemann commented 4 years ago

Thank you.

Can you confirm that using - (hyphen or dash) as an output filename is intended to go to stdout ?

hsinnan75 commented 4 years ago

I've updated MapCaller to v0.9.9.29. It considers "-" as an output filename for stdout.