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Commits on Feb 13, 2016

• moved indexing to libbwa

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Commits on Nov 19, 2014

• r1005: insert arbitrary header lines

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Commits on Nov 18, 2014

• r998: smart pairing; allow mixture of SE/PE reads

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Commits on Oct 16, 2014

• replaced Sys V shm with POSIX shm

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Commits on Oct 15, 2014

• shm works on small files, but not large ones

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• shared memory

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• r898: read the index into a single memory block

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Commits on Apr 11, 2014

• dev-472: get rid of bwa_fix_xref()

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Commits on Mar 28, 2014

• dev-450: support diff ins/del penalties. NO TEST!!

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Commits on Mar 5, 2013

• move mem_fill_scmat() to bwa.{h,c}

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Commits on Feb 26, 2013

• r295: generate NM

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• r284: amend cross-reference hit

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Commits on Feb 24, 2013

• added a bit documentation

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Commits on Feb 23, 2013

• support read group in bwa-mem

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• cleanup index loading code

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  cfa7165

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• code refactoring

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• moved some common code to bwa.{c,h}

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Commits on Feb 12, 2013

• Multiple changes:

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Commits on Apr 8, 2012

• updated APIs abit

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• simplified bwa_se() interface

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  3b5a9e5

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• complete single-end alignment

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• preliminary doc

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• compute CIGAR; rev seq not working

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Commits on Apr 7, 2012

• towards refined gapped; unfinished

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• API: aln seems working

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