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bcgsc / NanoSim

Nanopore sequence read simulator
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Suggested HTSeq v0.12.4 compatibility changes #88

Closed cytham closed 4 years ago

cytham commented 4 years ago

Suggested changes to get_primary_sam.py script -Added header to prefix_primary.sam file -Substituted original_sam_line with get_sam_line() because original_sam_line returns empty string Note: For it to work, we need to wait for HTSeq to resolve issue https://github.com/htseq/htseq/issues/11 in commit 797f802

cheny19 commented 4 years ago

As mentioned in #85 , we already replaced HTSeq with pysam and added headers to primary alignment file, so we'll ignore this PR for now. Thanks so much for the effort!