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Commits on Jun 8, 2022

• modifying BAMReader to a modern HTSLib usage

  

  guilhermesena1

  committed
  9a79634

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Commits on May 26, 2018

• Fixed whitespace formatting

  andrewdavidsmith

  committed
  5b6c431

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• Fixed indentation two spaces per tab, removed trailing whitespace and removed whitespace from empty lines

  andrewdavidsmith

  committed
  b25c151

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Commits on Dec 27, 2017

• Fixed a typo in the verbose output

  andrewdavidsmith

  authored
  37c3b35

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Commits on Jul 26, 2016

• Fixed indentation as newer gcc complains about misleading indentation of if statements.

  andrewdavidsmith

  committed
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Commits on Oct 6, 2015

• Replacing the deprecated finite function with isfinite from stl

  andrewdavidsmith

  committed
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Commits on Aug 15, 2015

• Merge commit '259602fdc08ca9835dfc6871eb477c481b4d9b40' as 'src/smithlab_cpp'

  songqiang

  committed
  278adcd

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• remove smithlab_cpp submodule

  songqiang

  committed
  ee9682b

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Commits on Aug 14, 2015

• update to include samtools files and make it compile in newer versions of OSX

  songqiang

  committed
  5cd7ebd

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• remove samtools

  songqiang

  committed
  fd40c25

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• add smithlab as submodules

  songqiang

  committed
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Commits on Aug 12, 2015

• use conditional compilation to support mac os

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  songqiang

  committed
  b8f6afc

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Commits on Dec 21, 2013

• fix a bug in sort chromosome size file

  songqiang

  committed
  7641a43

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Commits on Aug 27, 2013

• use different sorting creterion for BAM files: chrom, start, end, strand

  songqiang

  committed
  c262e70

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Commits on Aug 21, 2013

• add unistd header to use getpid for seeding random number generators

  songqiang

  committed
  f90e9ef

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Commits on Aug 22, 2012

• fix a typo in outputing gap regions

  

  no_author

  committed
  c30bc6b

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• sort chromosome files names

  

  no_author

  committed
  3349b8b

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Commits on Aug 21, 2012

• add default value 5 for prefix_len

  

  no_author

  committed
  1fc8253

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Commits on Jul 19, 2012

• commit 95db412156e0cc395902ecc22f39639f327c682a

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  songqiang

  committed
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Commits on Mar 13, 2012

• Show description for 9c69b28
  songqiang

  committed
  9c69b28

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Commits on Jan 18, 2012

• Distro and SplitDistro has no implicit constructors. cannot resize distros

  songqiang

  committed
  e1ebbc7

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Commits on Jan 16, 2012

• two changes

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  songqiang

  committed
  ab93577

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• add ModelParams library

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  songqiang

  committed
  93a598d

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• output the first pair of unsorted reads

  songqiang

  committed
  fa32b87

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Commits on Jan 6, 2012

• determine the input reads file format with a commandline option instead of the file extension names

  songqiang

  committed
  a2817ea

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Commits on Jan 5, 2012

• hide infrequently used options

  songqiang

  committed
  fa4f970

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• fix a bug. the length of a read should be determined from cigers instead of simply using l_qseq

  songqiang

  committed
  a05c1fe

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• add samtools libraries

  songqiang

  committed
  904070d

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• Allow reads input file to be either .bam format or .bed format

  songqiang

  committed
  ad89b86

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• Add BAMFile class

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  songqiang

  committed
  5970c0d

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Commits on Jan 2, 2012

• Several additional modifications for clarity of command-line help.

  andrewdavidsmith

  committed
  9746dbb

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• More improvements to the command line help

  andrewdavidsmith

  committed
  27a1af2

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• Several fixes related to help output and command line parsing.

  andrewdavidsmith

  committed
  64c512d

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Commits on Dec 31, 2011

• remove deprecated code

  songqiang

  committed
  7cdc708

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• change the format of posterior score file for each bin

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  songqiang

  committed
  eb3a50d

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