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yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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fixing samtools sort output #111

Open baileyglen opened 7 years ago

baileyglen commented 7 years ago

Samtools sort was missing the -o argument, which didn't work with current versions of samtools. I believe this fix will work starting with samtools 1.0 forward. May not work with earlier samtools. Could add in a samtools version check. This resolves Issue 107, and perhaps 91. Has been tested locally.

baileyglen commented 7 years ago

This is my first attempt at contributing to an open source project, so hopefully I am doing it correctly.

baileyglen commented 7 years ago

So...I had to make a second commit, and have found a potential issue with the test suite. Basically, the output files aren't being cleared. This test has probably been passing even with updated versions of samtools, but when the sort failed, it didn't create a new bam, but the test suite does not clear the existing files, so the tests pass as long as they have passed previously.