Gzip vcf files before tar/md5 process
bgzipping vcfs is optional
Merge branch 'master' of github.com:genome/genome into tcga_bgzip
Fix test data
The sdrf file now contains the compressed vcf name if appropriate
add "make_header_line" function to G/F/Bedpe/Header

When called on an empty header, the proper header line will be generated
and added (including the standard and any custom fields).

When called on a non-empty header, an exception is thrown.
update G/F/Breakdancer to be able to parse Squaredancer files

Squaredancer reports SVs in Breakdancer format with one notable
exception: the orientation fields. Breakdancer always reports + and -
counts (even when one is zero):

    10+0-

Squaredancer can report for only one strand, like so:
    10+

The parsing code now handles both possibilities.
Merge pull request #309 from tabbott/sv-fileformats

Sv fileformats
bed reporter needs to write .bed file for igv xml to work
Merge pull request #296 from gsanders/tcga_bgzip

CreateSubmissionArchive bgzips vcfs before generating manifest
Merge pull request #311 from susannasiebert/variant_reporting_igv

Bed report needs to write .bed file for igv xml to work
add gmt bwa run-mem

A command to map fastqs to coordinate sorted bam files with bwa mem.