Adding the option to specify the sort order of an output SAM file produced by SamBuilder. #25
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## main #25 +/- ##
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+ Coverage 92.91% 93.01% +0.09%
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Files 30 30
Lines 3079 3119 +40
Branches 572 579 +7
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+ Hits 2861 2901 +40
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TedBrookings
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@nh13 In addition to the change you requested, I made three other notable changes
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| @@ -899,3 +900,14 @@ def __next__(self) -> Template: | |||
| name = self._iter.peek().query_name | |||
| recs = self._iter.takewhile(lambda r: r.query_name == name) | |||
| return Template.build(recs, validate=False) | |||
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| class SamOrder(enum.Enum): | |||
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Having looked at this many months later, I wonder if this is too simplistic (see our Scala equivalent: https://github.com/fulcrumgenomics/fgbio/blob/ff1ca67772c34a8defeb835d692a53ad6e536f74/src/main/scala/com/fulcrumgenomics/bam/api/SamOrder.scala#L172). It doesn't allow custom sort orders, including setting group order, sub-sort, etc. I am fine with this for now, but changing this later will require breaking changes, so lets require @tfenne to weigh in too.
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I would stop where we are - there's nothing here that would prevent us from doing something more sophisticated later.
* Add SamOrder enum consistent with SAM spec * Add _sort_order as private member of SamBuilder to avoid changes inconsistent with header * Update poetry environment for newer python Co-authored-by: Nathan Roach <nathan@fulcrumgenomics.com> Co-authored-by: Ted Brookings <ted@fulcrumgenomics.com>
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The support for
TemplateCoordinatesorted records is coming in the first wave of wrappedpysamsamtoolsdispatch calls.This should address #20.
This is also more or less identical to an addition made to samwell in a PR merged presumably after the sambuilder module code was pulled over from samwell to here.