Merge pull request #6 from ozemsbg/sample_genome

Implement sampled genome feature

- enhancement: aaftoolz (parallelization of composable analysis for A…

…AF files)

- enhancement: tool to collate alignment accuracy vs variant content vs MQ data
               from an AAF and write it out as a CSV

2.25.1

- bugfix: bam2illumina discards read with tlen = 0
  Also discards reads with tlen < 0.95 read len, which allows us to have some reads with tlen = rlen
  in the simulation (which tests some edge cases in the aligner) but not too many,
  which screws up our stats.
- bugfix: god-aligner now writes out tlen
  Does so matching the SAM spec.
- enhancement: new model illuminaHiSeq-FCA.pkl added
- bugfix: god-aligner now sets .mate_is_reverse too

docs: improved bam-to-truth documentation

1. Improved wording
2. Removed figures
3. Moved to Utilities section

d-err fix, MQ heatmaps, god-aligner V1 CIGAR

- bugfix: Fix to alignment scoring. Affects data with soft-clips and insertions
- bugfix: subset-bam: fixed v range to be inclusive
- enhancement: read count heatmap added to alignment analysis
- enhancement: read fate bar chart now has read count numbers
- enhancement: god-aligner outputs V1 CIGARs by default, V2 CIGARs if requested
- workaround: pysam.index is finicky (on Linux). Adding option to god-aligner to skip indexing
Used on the platform and on platforms where pysam.index is finicky

subset-bam tool, mean MQ heatmap added

Synthetic read model and read un-pairing implemented

New tools: call-fate, poor-alignments and numerous bug-fixes and impr…

…ovements to documentation.

Read lengths can be truncated to arbitrary lengths if needed.

New variant model: Copy Insertion, creates insertions that are copies of random parts of the reference sequence. These insertions are challenging to align to and assemble.

Batch of important bugfixes in analysis code and improvements to anal…

…ysis plots.