Bwa-Mem and tied pair-placements - #42

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boukn wants to merge 5 commits into

Commits on May 4, 2015

Added bwa_verbose lines for pairing stuff
boukn
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c68334b
mem_pair will now return ties in 'zv'
boukn
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c4f78b7

Commits on May 5, 2015

Added to mem_sam_pe, support for putting the ties in the SAM output
boukn
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9d40fc3
Bugfixed the ties, for secondary flags and stuff.
boukn
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b5e0e62

Commits on May 6, 2015

Indent fixes
boukn
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3eeb802