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Two patches for OSX portability #56

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merged 2 commits into from May 9, 2017

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wltrimbl commented Apr 6, 2017

  1. Apple's gzip does not support --rsyncable. This causes five tests to fail on OSX, specifically join test 3, mcf tests 18-19, and multx tests 4-6.
$ head -n 4 t/tmp/mcf.t.*/test6.err
gzip: unrecognized option `--rsyncable'
  Apple gzip 251
  usage: gzip [-123456789acdfhklLNnqrtVv] [-S .suffix] [<file> [<file> ...]]
   -1 --fast            fastest (worst) compression

One option is to replace apple's gzip
https://www.drupal.org/node/1901508
this PR removes the --rsyncable option from gzip for portability.

  1. There is a problem with getline.c that fails to allocate memory for the null terminator when the line length is a multiple of 64. After porting to OSX, one of the tests failed with corrupt fastq when successive calls to read_line overwrote and corrupted data already in the fq structure. This was an off-by-one error in the test to see if getstr should allocate more memory.

@ExpressionAnalysis ExpressionAnalysis merged commit e556e16 into ExpressionAnalysis:master May 9, 2017

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