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Commits on Feb 12, 2020

• minor

  shilpagarg

  committedFeb 12, 2020
  db7529b

Commits on Jan 31, 2020

• increased buffer size globally and for fragment lines

  pjedge

  committedJan 31, 2020
  eecb8b9

Commits on Dec 1, 2019

• a line

  pjedge

  committedDec 1, 2019
  639a34e

• potential tenx genomics bug fix

  pjedge

  committedDec 1, 2019
  a973f0c

Commits on Nov 6, 2019

• Update README.md

  pjedge

  committedNov 6, 2019
  de33b57

• changes to makefile

  pjedge

  committedNov 6, 2019
  cffdf4b

• Removed submodules

  pjedge

  committedNov 6, 2019
  9b8714c

• first commit without htslib in makefile

  pjedge

  committedNov 6, 2019
  50df6a2

• fixed missing stdint include in readfasta.c

  pjedge

  committedNov 6, 2019
  4c95021

• Merge pull request vibansal#87 from jmarshall/htslib

  pjedge

  committedNov 6, 2019
  48bb718

Commits on Nov 4, 2019

• Merge pull request vibansal#85 from marcelm/shebangs

  pjedge

  committedNov 4, 2019
  23709fe

Commits on Oct 31, 2019

• Convert uses of legacy samtools API to use HTSlib API instead

  jmarshall

  committedOct 31, 2019
  a3b57ad

Commits on Oct 30, 2019

• Add shebangs to some Python utility scripts

  marcelm

  committedOct 30, 2019
  0ece7a1

Commits on Jun 10, 2019

• updated output VCF code

  vibansal

  committedJun 10, 2019
  16ca66c

Commits on May 24, 2019

• removed white-space in VCF output header

  vibansal

  committedMay 24, 2019
  fd01a1d

Commits on May 10, 2019

• minor edit to readme

  vibansal

  committedMay 10, 2019
  3931607

Commits on May 5, 2019

• fixed segmentation fault due to unallocated memory (reflist) being freed at the end of extracthairs.c

  vibansal

  committedMay 5, 2019
  22d3451

Commits on May 1, 2019

• calculate_haplotype_statistics now allows for VCFs without PS info (all variants are assumed to be in a single block) and gives a warning if no positions are compared for errors

  pjedge

  committedMay 1, 2019
  d04e51b

Commits on Apr 22, 2019

• fixed build issue caused by missing include in Makefile

  pjedge

  committedApr 22, 2019
  3cb79c1

Commits on Apr 6, 2019

• updated calculate_haplotype_statistics README for new PS flag requirement.

  pjedge

  committedApr 6, 2019
  53866c5

• Merge branch 'master' of https://github.com/vibansal/HapCUT2

  pjedge

  committedApr 6, 2019
  73958e5

• fixed bug causing calculate_haplotype_statistics.py crash if format fields too short due to missing PS in some unphased entries

  pjedge

  committedApr 6, 2019
  0c90038

Commits on Apr 4, 2019

• minor edit

  vibansal

  committedApr 4, 2019
  3363c1e

• update to README for new release

  vibansal

  committedApr 4, 2019
  c49cc7d

Commits on Mar 20, 2019

• Merge branch 'master' into realignment.

  vibansal

  committedMar 20, 2019
  5a6f5df

• 1. updated pHMM based realignment function (from longshot)

  vibansal

  committedMar 20, 2019
  e3c291e

Commits on Mar 14, 2019

• changed minimum --mbq to 4

  pjedge

  committedMar 14, 2019
  1ba3e87

• added check so that --mbq is not lower than 3, which can break haplotype calculation

  pjedge

  committedMar 14, 2019
  c50dede

Commits on Feb 21, 2019

• Update README.md

  vibansal

  committedFeb 21, 2019
  2dd17ad

Commits on Jan 23, 2019

• Update README.md

  pjedge

  committedJan 23, 2019
  b1e97f2

Commits on Dec 14, 2018

• minor cleanup

  vibansal

  committedDec 14, 2018
  9ba82da

Commits on Dec 11, 2018

• faster realignment for SMS reads (directly multiply probabilities instead of using log-space)

  vibansal

  committedDec 11, 2018
  a1a4325

Commits on Dec 6, 2018

• bug fixed in sum_all_alignments function

  vibansal

  committedDec 6, 2018
  bf1ac43

Commits on Dec 5, 2018

• branch:

  vibansal

  committedDec 5, 2018
  fff1f21

• updating realignment code

  vibansal

  committedDec 5, 2018
  d67822e

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