Speed improvements for job re-runs. Remove checking steps inside main output file checkpoints. #299
Add function to only return mapped reads from a BAM file.
Remove the merge SAM and FASTQ step after alignment.

STAR has an option to output the unmapped reads and Tophat
has a separate BAM file of unmapped reads. Both need to have
the read groups fixed on them, and Tophat has some additional
issues where the flags are not set properly on unmapped
mate pairs.
Finish writing the docstring for _fix_unmapped.
Handle in-place data dictionary updates from alignment as well as raw SAM output.
Remove unused function.
Support for latest bcftools and htslib release candidate: 0.2.0-rc6. Fixes #301
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add more helpful error message for bcbio installations where we cannot find data directory. Fixes #313
Add star attribute to test.

Now we can test Tophat and STAR separately.
Add more in depth description of the RNA-seq output.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Generalize reference detection to provide pointers for fasta files, reference indexes, plus aligner indexes. Enables shipping full analysis to non-shared filesystem by enumerating all requirements
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Have STAR set the read group tags.

This saves a call out to AddOrReplaceReadGroups. There is
an issue with it, though, that it creates a malformed header.
https://groups.google.com/d/msg/rna-star/xxE4cUnafJQ/EUsgYId-dB8J

A fix is in place to handle it for now and can be removed
if/when the bug is fixed upstream.

Added reheadering function for BAM files.
Use AlienTrimmer instead of cutadapt.

AlienTrimmer is much faster the way we are using it, at
least 10x faster. We do less trimming this way, and will
lose some reads but taking hours and hours to trim the
reads perfectly isn't worth the effort to recover a small
number of reads.
Fix for annotation for GTF files without standard fields.

This just bails out annotating the file.
Enumerate files needed for snpEff effects prediction so these can be transferred to individual processing nodes in non-shared filesystems
Enumerate alternative genomes used during validation to allow passing through to non-shared filesystems
Correct retrieval of alternative genomes for validation