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Commits on Feb 12, 2013

• merge bseq.{h,c} to utils.{h,c}

  Show description for 95d1844
  lh3

  committed
  95d1844

• code backup

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  committed
  13288e2

Commits on Feb 11, 2013

• separated and improved SAM printing code

  Show description for 99907c9
  lh3

  committed
  99907c9

• fixed a stupid bug in fastq reading

  lh3

  committed
  987d4b4

• code backup

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  committed
  59eaf65

Commits on Feb 10, 2013

• move sort_and_dedup() to worker1()

  lh3

  committed
  f4c0672

• a little refactoring for PE support

  lh3

  committed
  c310fb7

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

• more accurate chain weight

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  2848d30

• the previous change does not work... Fixed.

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  committed
  220fc39

• better dealing with microrepeat

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  fdb0a74

• exclude identical hits

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  committed
  057b292

• minor improvement to mapQ

  lh3

  committed
  1bf1a67

• minor improvement to mapQ approx.

  Show description for 245505d
  lh3

  committed
  245505d

• Don't use narrow band.

  Show description for d8e4d57
  lh3

  committed
  d8e4d57

• better treatment for micro-repeat

  lh3

  committed
  d890c79

• bugfix: when no seed hits found

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  45b0d34

• discard internal seeds shorter than half

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  cd6bd52

Commits on Feb 7, 2013

• compute mapQ; extend from the longest seed

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  committed
  83a49f3

• no effective changes

  lh3

  committed
  6ba11ab

• write soft clip; added debugging code

  lh3

  committed
  ff3fea1

• single-end working! no mapQ, though

  lh3

  committed
  27fdf63

• CIGAR is wrong, but the rest is okay

  lh3

  committed
  49f2bcc

• code backup

  lh3

  committed
  1fd51fc

• code backup

  lh3

  committed
  bfeb37c

• start to write CLI

  lh3

  committed
  5dc398c

Commits on Feb 6, 2013

• updated to the latest kseq.h

  lh3

  committed
  5a0b32b

• a bit code cleanup

  lh3

  committed
  a9292d6

• sorting chains while filtering chains

  lh3

  committed
  797a8c1

• separate CIGAR generation

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  committed
  a61288c

Commits on Feb 5, 2013

• fixed a silly bug in ksw_extend()

  Show description for 14e6a7b
  lh3

  committed
  14e6a7b

• calling ksw_global(); ksw_extend() is buggy!

  lh3

  committed
  1e16f3e

• fixed a silly bug on sorted merge

  lh3

  committed
  7067af8

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