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gt1 / biobambam2

Tools for early stage alignment file processing
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`bamsormadup` stalls if temp folder does not exist #79

Closed fgvieira closed 5 years ago

fgvieira commented 5 years ago

Hi,

found this issue when some of my bamsormadup runs would not finish.

I'd define a temp file (e.g. temp/run1/sample1.tmp) but, when some part of the path does not exist (e.g. /temp/run1 folder does not exist), it just stalls. I think it would be nice if it could print an error or just create all needed (sub-)folders.

cheers,

gt1 commented 5 years ago

Hi,

could you try

https://gitlab.com/german.tischler/biobambam2/tags/2.0.93-release-20190312162502

using

https://gitlab.com/german.tischler/libmaus2/tags/2.0.603-release-20190312152702

?

jmarshall commented 5 years ago

@gt1: Does this mean biobambam2/libmaus2 development has moved to GitLab? If so, a note in README.md and/or in the project description at the top of https://github.com/gt1/biobambam2 would be useful.

gt1 commented 5 years ago

@jmarshall: yes. I have added a note.

fgvieira commented 5 years ago

seems to work! thanks