| Date Y-m-d | Ticket | Description |
|---|---|---|
| 2019-06-14 | GT-804 | Simplify README and add static build |
| 2019-05-27 | GT-802 | Update license to Apache and fix docker entry |
| 2019-05-11 | GT-743 | Update interface and error handling | | 2018-12-11 | GT-696 | Fix newlines in validation scripts (public repo already fixed) |
| 2018-12-06 | GT-675 | Fix filters and alignment stats. Change depth test threshold on lower end | | 2018-11-08 | GT-660 | Optimize GQ for variant genotypes | | 2018-11-02 | GT-656 | Improvement for simple SV genotyping | | 2018-07-19 | GT-501 | Breakpoint depth test based on normal distribution | | 2018-07-16 | GT-539 | VCF now output genotypes for all samples in manifest and input VCF | | 2018-06-28 | GT-527 | --graph-sequence-matching yes fails with boost 1.63 |
| 2018-06-27 | GT-490 | Paragraph 2.0 release; disable Poisson depth test by default | | 2018-06-27 | GT-495 | Improved output of phasing information and paths | | 2018-06-26 | GT-402 | support genotyping on male chrX | | 2018-06-07 | GT-496 | -A still causes grmpy to run out of memory | | 2018-06-06 | GT-492 | -A causes grmpy to run out of memory | | 2018-05-31 | GT-491 | paragraph fails to compile with boost 1.53 | | 2018-05-31 | GT-484 | Output VCF with new genotypes as computed by grmpy | | 2018-05-31 | GT-477 | Add features to output alignment in multigrmpy and perform superlocus VCF splitting | | 2018-05-30 | GT-485 | Running GiaB VCF with klib alignment produces error message | | 2018-05-24 | GT-473 | Round floating point numbers in json output | | 2018-05-24 | GT-471 | Report read-counts for path families instead of paths | | 2018-05-24 | GT-476 | some command line parameters ignored in paragraph | | 2018-05-23 | GT-474 | support for command line location of graphtools source tree | | 2018-05-16 | GT-436 | post-process bad KmerAlignment results with smith waterman | | 2018-05-16 | GT-451 | Add path family based phasing and haplotype reconstruction | | 2018-05-15 | GT-445 | Add path aligner to produce faster alignments for exact matches | | 2018-05-14 | GT-462 | Minor fixes to vcf2paragraph.py for paralog graphs | | 2018-05-10 | GT-463 | vcf2paragraph fails to produce alt paths | | 2018-05-09 | GT-459 | Update to graph-tools 0.2.x | | 2018-04-23 | GT-450 | Local align Klib introducess odd soft clip | | 2018-04-25 | GT-454 | harmonize output options between paragraph and grmpy | | 2018-04-20 | GT-446 | Fix variant extraction due to bug in cigarToRefVar | | 2018-04-20 | GT-449 | performance lost due to recent merge making bam/cram open for each graph instead of once per thead-file | | 2018-04-19 | GT-447 | Fix multigrampy event ID | | 2018-04-16 | GT-439 | Fix logging + verbosity for multigrmpy.py | | 2018-04-16 | GT-438 | Fix high memory usage in grmpy and paragraph | | 2018-04-13 | GT-435 | Add support to vcf2paragraph.py for symbolic INS allele in SV VCFs | | 2018-04-13 | GT-437 | Fix multithreading race conditions | | 2018-04-11 | GT-353 | Refactor to use graph-tools library rather than protobuf | | 2018-04-07 | GT-417 | Refactor VCF to graph conversion |
| 2018-04-05 | GT-429 | option to turn off exact and graph aligners in grmpy | | 2018-04-05 | GT-428 | upgrade htslib to version 1.8 | | 2018-04-04 | GT-427 | GT-427 multigrmpy to generate graph ID if vc2toparagraph does not provide it| | 2018-04-03 | GT-415 | GT-415 use parallel grmpy in multigrmpy | | 2018-03-22 | GT-414 | Use filter instead of mapping status to decide whether to graph align after kmer aligner| | 2018-03-20 | GT-412 | Kmer aligner produces fully clipped nodes at start or end of the alignment| | 2018-03-20 | GT-407 | Refined edge filter | | 2018-03-15 | GT-403 | New threading for grmpy | | 2018-03-15 | GT-235 | Add documentation for read counting | | 2018-03-14 | GT-406 | Combine source and sink softclips with adjacent node CIGAR in KmerAligner| | 2018-03-11 | GT-398 | Minor grmpy fix and documentation update | | 2018-03-07 | GT-394 | graph-level threading to improve efficiency with high-latency file systems| | 2018-01-03 | GT-393 | Command line option for simulated reads coverage | | 2018-01-03 | GT-392 | Reads sometimes out of order in simulated.bam | | 2018-03-05 | GT-396 | Add command line options to specify location of BAM index separately | | 2018-02-28 | GT-388 | Improved genotyping on variants with different breakpoint genotypes |
| 2018-02-21 | GT-374 | support for read-level validation |
| 2018-02-19 | GT-379 | configure tool for installation |
| 2018-02-15 | GT-373 | Speedup bam processing by keeping the file open between the graphs |
| 2018-02-15 | GT-369 | Paragraph can align reads from multiple BAM files |
| 2018-02-15 | GT-365 | Add functionality to extract read-supported haplotype paths |
| 2018-02-09 | GT-360 | Add kmer-based aligner to paragraph |
| 2018-02-09 | GT-310 | Introduce kmer-based readfiltering, improve bad_align filter |
| 2018-02-07 | GT-294 | Add internal statistics function library, Gaussian fitting |
| 2018-02-06 | GT-352 | Support in paragraph for running multiple graphs in one go |
| 2018-02-04 | GT-345 | Refactor CMake sources, split out dependency compile process |
| 2018-02-01 | GT-306 | Improve build process, allow linking against paragraph as a library |
| 2018-02-01 | GT-318 | Genotyping parameters from external JSON |
| 2018-01-29 | GT-316 | Add graph validation statistics in output JSON |
| 2018-01-16 | GT-315 | Refactor genotyping code to allow joint genotyping inside grmpy |
| 2017-12-13 | GT-316 | Add more code for gapless read alignment |
| 2017-12-13 | GT-220 | Improve read extraction and increase target region size |
| 2017-12-11 | GT-304 | Add basic infrastructure for gapless alignments |
| 2017-12-07 | GT-305 | Update testing infrastructure + add Docker based tests |
| 2017-12-06 | GT-311 | Minor build fix for certain versions of g++ |
| 2017-11-30 | GT-308 | Improved documentation of genotyping model |
| 2017-11-28 | GT-292 | Add kmer index class and basic tools for graph indexing |
First release of SV genotyper with support for deletions, insertions, substitutions.