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* fix bug that caused mishandling of soft clipped reads * add performance test script * some better assertions * other minor fixes
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Tests successful on both python 2.7 and 3.4 for this. |
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I don't know if this is an insignificant style difference, but I usually define argument parsers at the global scope. Also, why do you need to get sys.argv[1:], wouldn't just parse_args() work?
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Sure, I can put the parser at global scope.
By doing sys.argv[1:] myself I have a function that I could theoretically call from other code, like tests, without assuming anything about the global argv
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Due to the issue pysam-developers/pysam#106 these changes require a snapshot pysam until a release is made. Once pysam makes a new release I'll update the dependency to use that.