Noah Spies

Or at least, make sure the heights are okay

- [ ] extra sample-specific args (sequencer, single_ended, split_hap) - [ ] parallelizing using `--first-` and `--last-variant`

For example, all the reads that map within a deletion are ignored currently

right now we're only including as unambiguous reads that overlap a *junction*, even though some segments may be unique (and this should be easy to tell)

Better handling of assembled contigs as input

1

- [x] need to be able to specify the alignment distance - [ ] check whether the alignments actually make sense - probably comparison between bwa and ssw would be...

- [ ] do a better job of picking ticks - [ ] improve labeling of ticks

Batch and log file destination

3

Is there any way to direct where the batch submission and log files get placed? If I specify a large number of jobs, my working directory gets filled with a...