[stats] Adjust a few counters by better filtering#1363
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whitwham merged 2 commits intosamtools:developfrom Jan 29, 2021
Merged
[stats] Adjust a few counters by better filtering#1363whitwham merged 2 commits intosamtools:developfrom
whitwham merged 2 commits intosamtools:developfrom
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include them in the orientation grouping counters (inward, outward, other).
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samtools statsnow displays the number of supplementary reads in theSN section. Also, supplementary reads are no longer considered when
splitting read pairs by orientation (inward, outward, other).
samtools statsnow counts only the filtered alignments that overlaptarget regions, if any are specified.
Fixes #1331
Fixes #1360