Releases: PapenfussLab/gridss
Releases · PapenfussLab/gridss
0.11.4
v0.11.3
Usability improvements:
- Reporting MAPQ > 60 as warning. Such values are typically from aligners that do follow the SAM specifications when reporting MAPQ
- Updated example script with java version check, and default hg19 blacklist
- INPUT_CATEGORY (IC) command-line arguments are now 1-based to match downstream analysis using the StructuralVariantAnnotation package
Additional VCF outputs:
- Reporting inexact homology lengths (max 300bp in either direction) in IHOMLEN field
- Using PARID instead of MATEID when writing VCF output
Performance improvements:
- Retaining cache of memoized paths between contig calls
- Removing partial misassembled contigs (too long to be valid breakend) during assembly instead of as post-assembly filter
- Not assembling when local graph complexity exceeds threshold (default threshold is 400 time median complexity of 500x coverage WGS sequencing).
Bug fixes/correctness improvements:
- Using language-independent locale
- Improved breakpoint positioning when inexact homology is present
- Incorporating RP/OEA anchor reads into assembly to enable longer assembly into the reference-supporting bases
- More conservative path collapse during assembly
0.10.1
Minor quality of life release
- --version now reports the version number
- Reduced log spam from metric and extraction steps (now only write log message every 10,000,000 read)
- Added default minimum event size of 32bp to reduce default output size. Configurable using variantcalling.minSize
- Graceful handling of invalid read alignments containing an insertion or deletion at the start or end of a read
0.10.0
This release contains a number of significant enhancements. Most important are:
- Handling of indels within read and assembly alignments (improved small event detection performance)
- Multiple scoring models. Alternative variant scoring models can be chosen by advanced users
- Added VcfBreakendToReadPair utility to help visualise calls
- Updated to htsjdk 2.0.1 for CRAM support
- Various bug fixes including correcting breakpoint orientation of spanned assembly compound events
v0.9.3
v0.9.2
v0.9.0
This version contains a number of features designed to improve usability including:
- simplified command line arguments - gridss algorithm parameters are now in their own properties file
- Unbounded number of input categories can be supplied - multi-sample analysis can now be done with more than just two categories
- ability to supply filter bed blacklist to improve assembly time by ignoring problematic centromeric
- In-process calling of external aligner during realignment steps - a wrapper script no longer needed
- bwa now supported as the external aligner during realignment steps
- LOW_QUAL filter added make default output usable without additional downstream filtering
- jar packaging and automatic loading of libsswjni.so