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Commits on Oct 11, 2017

• r500: temporarily disabled region trunc

  Show description for 65abdb8
  lh3

  committed
  65abdb8

• r499: end bonus working; DP region needs improve!

  lh3

  committed
  7345621

• r498: fixed a bug when merging like "4I5I"

  lh3

  committed
  ca632f9

Commits on Oct 10, 2017

• r497: the previous change not working at the ends

  lh3

  committed
  6c78a98

• r496: avoid DP extending into another chain

  Show description for c217eec
  lh3

  committed
  c217eec

• r495: fix impropriate CIGAR

  Show description for 13b66aa
  lh3

  committed
  13b66aa

• r494: simpler and better SR gap filling

  Show description for 46fa520
  lh3

  committed
  46fa520

• r493: reduced calling extd2 for ungapped aln

  Show description for 1e53610
  lh3

  committed
  1e53610

Commits on Oct 9, 2017

• r452: typo in the last commit

  lh3

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  9396d9e

• r491: an ambiguous base costs the same as gap ext

  lh3

  committed
  198849a

• r490: improved short-read extension heuristic

  Show description for 9fea4d1
  lh3

  committed
  9fea4d1

Commits on Oct 8, 2017

• r489: don't use approximate zdrop

  Show description for f941562
  lh3

  committed
  f941562

• r488: parameter to control max fragment length

  lh3

  committed
  61e56c9

Commits on Oct 7, 2017

• r487: demote "map10k"; improved README

  lh3

  committed
  f150257

• r486: treat "U" as "T" for RNA reads (lh3#33)

  lh3

  committed
  bf2d4f7

Commits on Oct 6, 2017

• minor wording changes

  lh3

  committed
  47b86e7

• completed README rewrite

  lh3

  committed
  56acf6e

• revamped README; not finished yet

  lh3

  committed
  4f6244b

• r482: increased short-read bandwidth to 100

  Show description for c6384ed
  lh3

  committed
  c6384ed

• 150bp mason2 simulation

  lh3

  committed
  2833a9c

Commits on Oct 5, 2017

• updated the mappy

  lh3

  committed
  de2fcc1

• r479: a bit code cleanup

  lh3

  committed
  e0baf1a

• r478: simplied useless code, a tiny bit

  lh3

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  f266092

• r477: renamed multi_seg to frag_mode

  lh3

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  9c5767f

• r476: multi-file fragment mode working

  lh3

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  ae2adf0

• r475: added --cs=none; updated manpage

  lh3

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  b839758

• r474: replaced -S and --cs-no-equal with --cs

  lh3

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  f4a5d3a

• r473: don't count introns into blen

  lh3

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  3ff6eda

• r472: fixed a bug when printing MAPQ/CIGAR

  lh3

  committed
  1a90bc8

• r471: all SAM features implemented; more tests!

  lh3

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  abf2a90

• more accurate SAM flag

  lh3

  committed
  5ab99eb

• r469: first step towards PE SAM

  lh3

  committed
  7cc4f6f

• r468: replaced ^ with ~ in cs

  lh3

  committed
  16e6e58

• r467: added : (equal length) and ^ (intron) ops

  lh3

  committed
  9aba117

Commits on Oct 4, 2017

• r466: detect multi-part index more smartly

  Show description for 7d50e64
  lh3

  committed
  7d50e64

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