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Commits on Jul 27, 2019

• Added some comments

  andrewdavidsmith

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• fixing the README

  andrewdavidsmith

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• Adding a README

  andrewdavidsmith

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Commits on Jul 26, 2019

• Adding autotools functionality

  andrewdavidsmith

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• Removing functions from GenomicRegion that are defined in chromosome_utils. These should probably be redesigned.

  andrewdavidsmith

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Commits on Jul 24, 2019

• Minor formatting changes

  andrewdavidsmith

  committed
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• Removing the SAM.hpp and SAM.cpp files; these are replaced with htslib_wrapper.hpp and htslib wrapper.cpp

  andrewdavidsmith

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Commits on Jul 21, 2019

• GenomicRegion: Fixing very old bug in parsing a 6 column BED file presented as a characer array

  andrewdavidsmith

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Commits on Jul 19, 2019

• Fixing arguments to ar and removing the headers from the archive

  andrewdavidsmith

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Commits on Jul 18, 2019

• Removing SAM2.hpp and SAM2.cpp as these are now in htslib_wrapper

  andrewdavidsmith

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• This now has the stuff from SAM2

  andrewdavidsmith

  committed
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• Fixing indentation

  andrewdavidsmith

  committed
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• Fixing indentation

  andrewdavidsmith

  committed
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• Change so that the insertion operators will work inside tostring

  andrewdavidsmith

  committed
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• GenomicRegion: updates to accommodate gzip functionality and modernization

  andrewdavidsmith

  committed
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Commits on Jul 13, 2019

• Added a peek function for the igzfstream. Wish this wasn't needed, but some of our line oriented reading requires checking for eof to avoid reading an empty line. This is included in the istream so…

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  andrewdavidsmith

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Commits on Jul 12, 2019

• Adding the static library for smithlab_cpp not intended to be used as a static lirary but to replace having to always specify so many object files

  andrewdavidsmith

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Commits on Jul 11, 2019

• Adding the zlib_wrapper.*pp files

  andrewdavidsmith

  committed
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Commits on Jul 5, 2019

• Adding updates to MappedRead for insertion and extraction operators to be consistent with future gz functionality

  andrewdavidsmith

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Commits on May 29, 2019

• SAM2: adding comment about why the line.l is reset to 0 after processing a read

  andrewdavidsmith

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Commits on May 28, 2019

• Adding the SAM2.hpp and SAM2.cpp which will hopefully replace the SAM.hpp and SAM.cpp files soon. The new versions directly use the libhts rather than the older samtools source

  andrewdavidsmith

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Commits on May 24, 2019

• Fixed #30.

  

  mengzhou

  committed
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Commits on May 23, 2019

• Fixing formatting for description of program in OptionParser

  andrewdavidsmith

  committed
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Commits on Apr 29, 2019

• Adding spaces to line length in help

  

  guilhermesena1

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Commits on Apr 27, 2019

• Fixed conflict

  andrewdavidsmith

  committed
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• Simplified the split whitespace function

  andrewdavidsmith

  committed
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• Fixed the parser for full paths into dir basename and suffix. Added a formatter to do the reverse

  andrewdavidsmith

  committed
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• Added a tostring function for MappedRead class

  andrewdavidsmith

  committed
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Commits on Apr 21, 2019

• Making a long-overdue simplification to the split whitespace function

  andrewdavidsmith

  committed
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Commits on Apr 14, 2019

• Changing the final condition in the report function for ProgressBar to be satisfied even if the original range is surpassed

  andrewdavidsmith

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Commits on Apr 7, 2019

• Might have the progress bar working...

  andrewdavidsmith

  committed
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Commits on Mar 16, 2019

• Adding code to indicate default option values. This should not break existing code that does not use this functionality.

  andrewdavidsmith

  committed
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Commits on Feb 17, 2019

• Reverting to a version with fewer bugs

  andrewdavidsmith

  committed
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Commits on Feb 16, 2019

• Cleaned up poor formatting

  

  andrewdavidsmith

  committed
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Commits on Jan 14, 2019

• ProgressBar: fixed the ordering of the variables that are defined in the constructor.

  masarunakajima

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