Make name sort put primary reads before secondary reads.#2012
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For validation, I've just been doing some perl one-liner hackery to summarise the samtools view outputs. Eg: |
For completeness, we consider non-secondary supplementaries as before secondaries, and non-supplementary secondaries before secondary+supplementary. This is because a (non-2ndary) supplementary read is a continuation of the primary read and should be grouped before alternate alignments for this read. We still have all READ1 data before all READ2 data, so the primary alignment has not changed ordering. This is simply a better way of resolving ties than keeping the original ordering. Fixes samtools#2010
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For completeness, we consider non-secondary supplementaries as before secondaries, and non-supplementary secondaries before secondary+supplementary.
This is because a (non-2ndary) supplementary read is a continuation of the primary read and should be grouped before alternate alignments for this read.
We still have all READ1 data before all READ2 data, so the primary alignment has not changed ordering. This is simply a better way of resolving ties than keeping the original ordering.
Fixes #2010