Tidy up FreeBayes

[fnothaft]

• bump to quay.io/ucsc_cgl/freebayes:1.1.0--f7597a50b4449d4a963ace565a6ca7040ae10118
• mount reference file into docker container
• support copying files to executor
• run in -i mode
• specify -region when invoking FreeBayes not necessary
• VCF comes out mis-ordered
• use Avocado read/contig filtering mechanism (Open up PrefilterReads for use externally avocado#254)

[heuermh]

Can we include test resources from https://github.com/ekg/freebayes/tree/master/test/tiny here in cli/src/test/resources? MIT License but the test data don't have a copyright notice to include.

[heuermh]

With the fix for bigdatagenomics/avocado#254 (commit bigdatagenomics/avocado@5f720cf), do you intend that Cannoli would depend on Avocado?

[heuermh]

Taking a closer look at the freebayes command line arguments, we should always use

   --strict-vcf
                   Generate strict VCF format (FORMAT/GQ will be an int)

and should provide arguments in the Freebayes wrapper for

   -A --cnv-map FILE
                   Read a copy number map from the BED file FILE, which has
                   the format:
                      reference sequence, start, end, sample name, copy number
                   ... for each region in each sample which does not have the
                   default copy number as set by --ploidy.

   --gvcf
                   Write gVCF output, which indicates coverage in uncalled regions.

   --gvcf-chunk NUM
                   When writing gVCF output emit a record for every NUM bases.

As to the rest, I'm not sure if we should wrap all of them, or provide a bulk argument/config mechanism, or simply say if you need to provide non-default parameters, call pipe manually.

[heuermh]

Fixed by #107.