more fixes for DHGT

v0.2.3

• for snps add 0's to DHGT if none overlap. previously the DHGT field was not added unless there were any snps overlapping the SV.

fixes for manta

This release updates htslib (which should give small speed improvements)
and it adds more/better support for manta and likely other callers.

fix for small SV start

v0.2.1

• fix for start of SV less than 99th percentile of insert size distribution (#28, #29, thanks @roryk)

fix tag and small updates

previous release was tagged incorrectly. code changes since then are minimal.

more SVTYPEs and flush stdout

v0.1.5

• support for more ALT types (e.g DUP:TANDEM, DEL:ME, etc)
• flush stdout properly (#25)

Installation

The binary duphold_static is the recommended way to use duphold. It is a static binary with no dependencies and will work for nearly all uses.

There is also a docker image available under brentp/duphold:v0.1.5

v0.1.4

v0.1.4

• output DHSP for BND elements on same chrom
• fix for #22: allow GQ of type Integer or Float
• fixes for SNP data (thanks Pierre for finding these)

Installation

• The binary duphold_static is the recommended way to use duphold. It is a static binary with no dependencies and will work for nearly all uses.
• The binary duphold_shared

/duphold_shared) depends on libhts.so for cases when a user wants to access bam/cram /vcf directly over S3 or https.

static build

this release has minor changes to the way that SVs are annotated with SNPs (to indicate LOH). It also comes with a static binary.

v0.1.3

• add DUPHOLD_SAMPLE_NAME environment variable as a way to set the sample name. (#19)
• re-vamp SNP stuff so that only DHGT is reported. It is an Integer with 5 columns for numbers of
  0. hom-ref 1. het 2. hom-alt 3. unknown 4. low-quality snp variants within each event.

Installation

• The binary duphold_static is the recommended way to use duphold. It is a static binary with no dependencies and will work for nearly all uses.
• The binary duphold_shared depends on libhts.so for cases when a user wants to access bam/cram /vcf directly over S3 or https.

flank changes. general improvements.

v0.1.2

• remove PCRE dependency.
• reduce logging output.
• support un-indexed VCFs without contig definitions.
• use only PASS SNVs from --snps
• set DHFFC flank distance to 1000 default (was 5000) and allow setting via DUPHOLD_FLANK env var and only use non-zero values in DHFFC flank. These 2 changes should improve DHFFC for samples with sparse coverage (e.g. for genomes without good assemblies). (Thanks @JoWhi for reporting and providing a test-case)

bugfix

v0.1.1

• fix bug when later chroms had larger values (see: 9f88400 and thanks @raul-w for reporting and providing a test-case).
• adjust calculation of global and per-gc bin coverage to use only non-zero bases. this improves the ratio when comparing
  to the depth inside of events (which will still count zero-coverage bases) in chromosomes with sparse coverage. (thanks @raul-w
  for suggesting).

reduce memory usage

v0.1.0

• reduce memory usage in discordant calculation.