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Commits on Oct 30, 2018

• r866: fixed a typo; resolves lh3#262

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  42baf28

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Commits on Jun 19, 2018

• r792: fixed -Wextra warnings and resolved lh3#184

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  7e6e8ca

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Commits on Nov 1, 2017

• r546: minor mapQ tuning

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  22290db

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Commits on Oct 31, 2017

• r544: increased PE mapQ

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  b8e758d

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Commits on Oct 16, 2017

• r512: option to filter poorly aligned reads

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  e6f525e

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Commits on Oct 13, 2017

• r511: fixed wrong primary sam record

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Commits on Oct 5, 2017

• more accurate SAM flag

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Commits on Oct 4, 2017

• r464: fixed a bug in pairing, due to randomization

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  19c39e7

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• r462: SAM primary flag not properly set

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• r461: randomize repetitive hits

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Commits on Sep 28, 2017

• r450: differentiate exact repeats via mapq

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  935a6e6

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• r448: fixed a bug when computing PE quality

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Commits on Sep 27, 2017

• r447: paired-end mapping quality

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  lh3

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• r445: pair coordinate adjustment working

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  lh3

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• r444: changed the way orientation is specified

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Commits on Sep 26, 2017

• r440: better chain filtering for PE reads

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  55d1e4f

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