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Commits on Mar 6, 2013

• r332: added output threshold

  Show description for 5fbd454
  lh3

  committed
  5fbd454

Commits on Mar 5, 2013

• r324: a little code cleanup

  Show description for efd9769
  lh3

  committed
  efd9769

• r323: added Z-dropoff, a variant of blast's X-drop

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  e0991d6

Commits on Mar 4, 2013

• code backup; more changes coming later

  lh3

  committed
  59bc934

Commits on Mar 1, 2013

• r315: move kopen.o out of libbwa.a

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  committed
  35fb7f9

• r314: cleanup bwamem API

  Show description for 3e4a178
  lh3

  committed
  3e4a178

Commits on Feb 28, 2013

• r309: bugfix - soft clipping missing in example.c

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  6a4d8c7

• r308: added a new API to convert region to CIGAR

  Show description for df7c3f0
  lh3

  committed
  df7c3f0

• r306: introduce clipping penalty

  Show description for 4bb0bdd
  lh3

  committed
  4bb0bdd

Commits on Feb 26, 2013

• r292: fixed a very stupid bug on CLI

  Show description for c6b226d
  lh3

  committed
  c6b226d

Commits on Feb 25, 2013

• r279: for PE mapq, consider the number of pairs

  Show description for 20aa848
  lh3

  committed
  20aa848

• r278: don't perform too many mate-sw

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  9957e04

• optionally mark split hit as secondary

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  5ead86a

Commits on Feb 24, 2013

• output multiple hits

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  85775c3

• added a bit documentation

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  6bdccf2

• simplified bwamem.h

  Show description for ee59a13
  lh3

  committed
  ee59a13

Commits on Feb 23, 2013

• moved some common code to bwa.{c,h}

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  e613195

Commits on Feb 22, 2013

• pring paired-end SAM

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  17c123d

Commits on Feb 21, 2013

• generate multiple alignments from one chain

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  a578688

• extend more seeds (and thus slower...)

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  54da54f

• Well, at least output sth

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  5626fe2

Commits on Feb 19, 2013

• code backup

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  committed
  688872f

Commits on Feb 18, 2013

• code backup

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  committed
  66585b7

Commits on Feb 14, 2013

• better and proper way to infer orinentation

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  df1ff2b

Commits on Feb 12, 2013

• code backup; to upgrade ksw.{c,h}

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  604e3d8

• keep track of the "parent" of a secondary

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  cd09693

• mark primary, instead of dropping secondary

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  22b79b3

• merge bseq.{h,c} to utils.{h,c}

  Show description for 95d1844
  lh3

  committed
  95d1844

Commits on Feb 11, 2013

• separated and improved SAM printing code

  Show description for 99907c9
  lh3

  committed
  99907c9

• code backup

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  committed
  59eaf65

Commits on Feb 8, 2013

• missing identical hits; improved sub_n

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  committed
  829664d

• consider the number of suboptimal hits

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  b2c7148

• allow more seeds to be seen (thus slower..)

  lh3

  committed
  3960706

• better dealing with microrepeat

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  fdb0a74

• minor improvement to mapQ

  lh3

  committed
  1bf1a67

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