Added is_sequence and is_pair for checking if input is from paired end
sequencing or not.
Merge branch 'master' of https://github.com/chapmanb/bcbb
Added split_vcf plus a unit test.
Merge branch 'master' of https://github.com/chapmanb/bcbb
Added Tophat 2 support.
Switched from throwing exceptions to exiting since there is nothing to handle.
Merge pull request #64 from roryk/master

Tophat2 support, vcf splitter by chromosome, some utilities.
Move splitting VCF functionality into split namespace
Provide support for configuring with debian/ubuntu's picard-tools package or a Picard download of jar files. Thanks to @guillermo-carrasco.
Provide distributed task for re-writing recalibrated BAM files. Provides parallel speed up when recalibrating on whole genome BAMs
Provide general mechanism to group together samples for concurrent processing. Use this to implement multi-sample GATK calling. Handles calling plus split and recombine into final single sample VCFs
Write documentation for distributed phylogenetic BLAST. Provide ability to process local pre-downloads FASTA dbs. Handle errors with no descriptions of recent blast+ versions
Added reading option list from tophat resources.
Improve naming for grouped variant calling: batches instead of families
Added arbitratry options passing.
Refactor to make it easier to follow.
Support variant calling with mpileup and VarScan, which uses a heuristic/statistic calling approach
Merge pull request #65 from roryk/master

Generic options support
Convert VarScan indel format into VCF compatible representation. Use local temporary directories by default for GATK runs
Avoid additional filtering for VarScan calls since calls are filtered as part of calling process