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genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
GNU General Public License v3.0
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Convert pindel to use the HTSlib API instead of the legacy samtools API #12

Closed jmarshall closed 9 years ago

jmarshall commented 9 years ago

This pull request converts the pindel source code to use HTSlib for its BAM-reading needs rather than the old samtools 0.1.x API. Since the old API is unmaintained (and has been for several years), I would suggest converting wholesale as in this PR rather than complicating the code by retaining the option to use either old-samtools or htslib.

Using the currently-maintained API will fix bugs such as #9; using the better-packaged htslib will fix issues #3 and #10 and remove the need for such as #11.

This now compiles, but I have not tested it.

Still to do:

Eventually README.md and INSTALL will need to be updated to talk about HTSlib instead of Samtools too.

EWLameijer commented 9 years ago

Okay... I've merged the pull request. I don't expect really funny things to happen, but I've discussed with Kai and he may be able to test it somewhere the coming days.