0.4.0

• Allow lower case reads in fastq files (previously, this would result in corrupt BAM files.
• HTSlib is now a submodule in the Github repository. This simplifies compilation. Further, that is the only supported compilation method now (samtools-0.1.19 is no longer supported).
• Somehow, the methylation extractor was still defaulting to a minimum phred score of 10, when the documentation said it was defaulting to 5.
• CRAM files can now be produced and processed. Both bison and bison_herd will output in CRAM format if the -C option is given.
• The header @pg line is now rewritten to contain the actual command executed and the bison/herd version.
• Excess space allocated to hold the genome is now returned.
• Output BAM/CRAM files can now be sorted on the fly. The method for this is similar to that used by samtools, where temporary files are written and then merged. This merge step is performed in parallel if multiple output files are being written by bison_herd.
• Fixed a bug in bison_CpG_coverage, where previously only the first chromosome was used.