Add trgt to process_sample

[williamrowell]

• trgt runs on merged, haplotagged BAM using regions in BED file in reference/ dir
• generates vcf.gz and spanning.bam
• uses trgt v0.3.4
• also generates a text file indicating regions in bed file that are not covered well in input BAM

[williamrowell]

Closes #121

[williamrowell]

Tested on 10Mbp on p23. Works as expected. New outputs are:

• {sample}.{ref}.trgt.spanning.bam
• {sample}.{ref}.trgt.vcf.gz
• {sample}.{ref}.trgt.vcf.gz.tbi

All are unsorted, direct output from trgt.

[williamrowell]

Assess whether regions in the trgt BED file have dropped out, based on aligned coverage.

New output:

• {sample}.{ref}.trgt.dropouts.txt

Columns:

• chrom
• chromstart
• chromend
• label
• FullDropout / HaplotypeDropout