samtools/htsjdk — pull request #89 by bpow (2014-08-30 02:18:12+00:00)
Title: SAMFileMergerTest relies on HashMap ordering produced by jdk6/7

The test files used by SAMFileMergerTest work under jdk6 and 7, but not under jdk8. There must be something about the hashing order produced in the different implementations that differs, because under jdk8, some of the attributes within the header lines end up in different orders (under jdk6&7, note that the input files `@RG` lines have SM before PL, but the expected output file has PL before SM. The SAM format does not require a specific order of attributes within a header line, so order should not matter from a testing perspective.

In the process of looking into this I also noticed that the test data files have some attributes in their `@SQ` lines separated by spaces. The SAM format specifies tab-delimited fields.