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SAMTextWriter.setSortOrder is not called before SAMTextWriter.setHeader in SAMRecordWriter #21

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ryan-williams opened this issue Aug 24, 2015 · 0 comments · Fixed by #22
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SAMTextWriter.setSortOrder is not called before SAMTextWriter.setHeader in SAMRecordWriter #21

ryan-williams opened this issue Aug 24, 2015 · 0 comments · Fixed by #22

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@ryan-williams
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SAMTextWriter.setSortOrder is not called before SAMTextWriter.setHeader in SAMRecordWriter.init, despite this comment stating that it must (link is from htsjdk 1.118, but this API and comment still exist in htsjdk 1.138).

I noticed this because all .sam output files in ADAM have @HD lines with a SO:unsorted tag, even if we set a coordinate sort on the SAMFileHeader before writing.
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set SortOrder before header on SAMTextWriter ryan-williams/Hadoop-BAM
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