Adding the option to specify the sort order of an output SAM file produced by SamBuilder.

[NatPRoach]

The support for TemplateCoordinate sorted records is coming in the first wave of wrapped pysam samtools dispatch 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.

[nh13]

minor comments

[codecov-commenter]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (273c81c) 92.91% compared to head (ae5b948) 93.01%.

Files	Patch %	Lines
fgpyo/sam/builder.py	87.50%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #25      +/-   ##
==========================================
+ Coverage   92.91%   93.01%   +0.09%     
==========================================
  Files          30       30              
  Lines        3079     3119      +40     
  Branches      572      579       +7     
==========================================
+ Hits         2861     2901      +40     
  Misses        145      145              
  Partials       73       73              

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[TedBrookings]

@nh13 In addition to the change you requested, I made three other notable changes

1. I updated the poetry environment to succeed in more recent python environments.
2. I removed the None option for sort_order. Unsorted and Unknown are both options and it feels messy to have None kicking around in there too.
3. I allowed writing with Unknown sort order, since it's in the spec. It's the same as Unsorted in its effect. This feels marginal to me, and I think you might feel strongly about removing it, so I wanted to draw attention.

[nh13]

Having looked at this many months later, I wonder if this is too simplistic (see our Scala equivalent: https:/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.

[tfenne]

I would stop where we are - there's nothing here that would prevent us from doing something more sophisticated later.