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Commits on Nov 30, 2011

• * printing primary index

  iontorrent-dev

  committed
  29def59

Commits on Nov 29, 2011

• * adding % completion in bwt index

  iontorrent-dev

  committed
  48e5706

• * adding option to print SA in the check

  iontorrent-dev

  committed
  52cef7a

• * adding bwt check, to check the consistency of the bwt index

  iontorrent-dev

  committed
  5c30439

Commits on Nov 28, 2011

• Release bwa-0.6.1

  

  Heng Li

  committed
  91a4a0c

• bugfix: bwa-sw PE segfault in rare case

  

  Heng Li

  committed
  64e353c

Commits on Nov 25, 2011

• fastmap: optionally output the original query seq

  

  Heng Li

  committed
  bf65b64

• fixed a deadlock; SMEM iterator

  

  Heng Li

  committed
  150bfbd

Commits on Nov 24, 2011

• output the NM tag

  

  Heng Li

  committed
  b5170e0

• fixed a minor issue in trimming

  

  Heng Li

  committed
  717959e

• perhaps improves samse/sampe

  

  Heng Li

  committed
  eeedda1

• optionally mark multi-part hits as secondary

  

  Heng Li

  committed
  196b50d

• reordering BWA-SW command-line prompt

  

  Heng Li

  committed
  9f84384

• removed a useless bwa-sw CMD option

  

  Heng Li

  committed
  b17b657

• incorrect mate pos in BWA-SW SE mode

  

  Heng Li

  committed
  107a987

• fixed a long-existing bug in trimming

  

  Heng Li

  committed
  dec584d

Commits on Nov 20, 2011

• useless script

  

  Heng Li

  committed
  84aa3fa

• use standard SW when no SSE2

  

  Heng Li

  committed
  182cb2e

Commits on Nov 19, 2011

• avoid duplicated XA tags

  

  Heng Li

  committed
  dc40089

Commits on Nov 18, 2011

• fixed a segfault when there are too few good bases.

  

  Heng Li

  committed
  8f89f55

Commits on Nov 13, 2011

• added SEAL

  

  Heng Li

  committed
  c8edcaf

• updated README

  

  Heng Li

  committed
  162f220

• remove a useless file

  

  Heng Li

  committed
  9f2c778

• Release BWA-0.6.0

  

  Heng Li

  committed
  770a5f2

Commits on Nov 12, 2011

• updated manual

  

  Heng Li

  committed
  f1517b8

• updated revision number

  

  Heng Li

  committed
  7544aca

• bugfix: bwa-short MT does not work (by Peter)

  

  Heng Li

  committed
  2f3cdcd

• crash under non-typical setting (by John Marshall)

  

  Heng Li

  committed
  56a1865

• multithreading works again

  

  Heng Li

  committed
  8060693

• bugfix: wrong mapping quality

  

  Heng Li

  committed
  fa8cfe5

• proper mate information

  

  Heng Li

  committed
  b42910a

Commits on Nov 7, 2011

• bwa-sw PE seems working (SAM is incorrect)

  

  Heng Li

  committed
  e06685d

Commits on Nov 6, 2011

• mate rescue seems working (not MT)

  

  Heng Li

  committed
  c8c79ef

• compute insert size distribution

  

  Heng Li

  committed
  17eaac5

Commits on Nov 5, 2011

• further preparation for pairing

  

  Heng Li

  committed
  a29b179

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