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