drop DHD in favor of DHFFC (flank-fold-change)

v0.0.9

• drop DHD in favor of DHFFC for (F)lank fold change.
• make changes to support long, single-end reads.
• fix bug in hts-nim that made duphold grab the wrong sample info from a SNP BCF (not vcf)

CRAM speed and optional annotation with snp/indel

v0.0.8

• skip duphold calculation for distant or interchromosomal BND's
• don't decode CRAM qname. This makes duphold use ~15% less CPU for CRAM
• allow annotating SVs with SNP calls as a additional validation of each event.

general improvements

duphold generally now uses median instead of mean. this makes it less susceptible to outliers and less sensitive to variant calls that are not exact.

the cutoffs for DHD are now data-driven.

v0.0.7

• remove DHBZ for the z-score. this was less useful than the fold-change values.
• greatly improve DHD. the cutoffs for this are now data-driven so that we expect a low false-positive rate
  of ends that are called to have a rapid change in depth. this requires an extra pass over each chromosome that
  will add about 90 seconds of runtime per (human or similar-sized) genome.
• DHBFC is now based on the median instead of mean so it is less susceptible to outliers and off-center calls
• fix bug that in rare cases resulted in exiting with "how"
• also report DHSP for number of supporting read-pairs for the event. This is usually redundant with SVTyper info, but might
  be more accurate in some cases.

improvements for BND

v0.0.6

• duphold will now annotate the space between BND's that occur within 20MB on the same chromosome. Sometimes events that are obvious
  deletions by their change in coverage will be called as a pair of BNDs. This will help prioritize those that are accompanied by a
  depth change.

bug fixes for variants near ends of chrom.

v0.0.5

• fix bug that occurred with SVs near either end of chromosome (#2). thanks Brad for reporting and providing a test-case.

small bug fixes and new flag to support per-sample parallelization.

v0.0.4

• small bug-fixes
• duphold now uses about half as much memory
• add -d/--drop flag which will drop all samples from a VCF except the
  one matching the sample in --bam. this simplifies per-sample
  parallelization followed by (bcftools) merge.

An impending release of smoove will support parallelization of duphold calls for multiple sample bams.

bugfixes and CLI change

v0.0.3

• fix bug when annotatign multi-sample vcf (#2)
• get sample name from bam read group info. NOTE that this changes the command line parameters by removing the --sample argument.

break-point depth-change and bugfixes

duphold now outputs and additional tag:

• DHD: rapid change in depth at one of the break-points (1 for higher (DUP). 0 for no or conflicting changes. -1 for drop (DUP), 2 or -2 for both break points)

good DUP calls will have values of 1 or 2 for DHD and DEL calls will have values of -1 or -2.

DHD corresponds to the rapid depth change you see by eye with IGV or samplot for obvious DUP/DEL calls.

initial release

this is an early release for intrepid users wanting feedback.