- Updated rtgtools to v3.12.1
- Defect remains: https://jira.illumina.com/browse/HAP-373. Use stable som.py v0.3.10.
- Fixed issues created by previous change to convert_gvcf arguments
- Removed redundant truth and query gvcf parameters in pre.py.
- som.py no longer hangs; fp.filtered SNV counting is incorrect. https://jira.illumina.com/browse/HAP-373. Use stable som.py v0.3.10.
| Ticket | Description |
|---|---|
| HAP-355 | Ensure compatibility with genome VCF from DRAGEN pipelines |
| HAP-356 | quantify module throws regex error |
| HAP-357 | Deal with change in Java license terms |
| HAP-359 | Hap.py crashes when ingesting variants genotyped as <NON_REF> |
| HAP-360 | Apply non-ref filter to truth set when --preprocess-truth is set |
| HAP-361 | Hap.py "blocksplit" processes still failing on DRAGEN gVCFs even with pre-filtering NON_REF genotypes |
| HAP-362 | Hap.py blocksplit sometimes crashes with "invalid next size (fast)" error |
| HAP-363 | Use 'git describe' to obtain version number during Cmake |
| Ticket | Description |
|---|---|
| HAP-341 | Update rtgtools to 3.10.1 |
| HAP-342 | som.py output tables to quantify / GA4GH format |
| HAP-346 | src/sh/illumina-setup.sh out of date |
| HAP-352 | string formatting in som.py: last interval is always [1.0, 1.0] in *extended.csv |
| Ticket | Description |
|---|---|
| HAP-326 | Support Pisces VCFs in som.py |
| HAP-332 | Fix bug in install.py related to external dependencies |
| HAP-333 | Update rtgtools to 3.8.2 and add support for distance-based matching |
| HAP-336 | Change Dataframe.sort to sort_value in som.py (#21) |
| Ticket | Description |
|---|---|
| HAP-317 | Update htslib to 1.4.1 and always check for BCF conversion errors |
| HAP-318 | Update rtgtools to 3.8.1 |
| HAP-319 | Slimmer docker image without hg19 reference |
| Ticket | Description |
|---|---|
| HAP-291 | Upgrade rtgtools dependency to version 3.7.1 |
| HAP-292 | Improve Dockerfile and update compiler requirements |
| HAP-295 | Preserve INFO fields when running with vcfeval comparison engine also |
| HAP-296 | Don't fail when no reference is found in default locations, just require -r |
| HAP-298 | Output run and session info in prefix.runinfo.json |
| HAP-299 | Improve command line documentation for confident regions. |
| HAP-300 | Correct documentation for --adjust-conf-regions |
| HAP-306 | Add distance-based matching method to assess discovery separately from genotyping |
| Ticket | Description |
|---|---|
| HAP-195 | Safer left-shifting and test for leftshifting-related issues added |
| HAP-259 | Som.py alternative GA4GH-based workflow: hap.py --engine scmp |
| HAP-266 | Optional new insertion handling: both surrounding bases must be covered to capture |
| HAP-267 | Add confident region overlap counts to stratification regions |
| HAP-268 | Fix bamstats.py (missing imports, now working) |
| HAP-270 | Handle special chars in input filenames better |
| HAP-274 | Issue #10 allow hap.py to be symlinked |
| HAP-275 | Somatic mode for hap.py comparisons added: --somatic switch squashes ploidy |
| HAP-276 | List-of-float INFO fields were getting rounded to int |
| HAP-279 | Issue #11 Output error message when preprocess fails |
| HAP-280 | Add Subset.Level column to stratified output, stratify into exons and genes |
| HAP-281 | Quantify precision and recall separately at truthset boundaries |
| HAP-282 | Output stratified counts also when regions are empty |
| HAP-285 | Hapenum outputs individual variants used in haplotype construction |
| HAP-286 | MacOS X build failure fixed |
| HAP-287 | Report F-score in summary CSV and also in summary output |
| HAP-288 | Read vcfeval SDF file from same path as fasta file if present |
| Ticket | Description |
|---|---|
| HAP-258 | Som.py avoid CI failure for empty subsets |
| HAP-260 | Add Dockerfile based on Centos 6 |
| HAP-261 | Som.py FP rate calculation only uses truth contig sizes |
| HAP-263 | Som.py fix AF binning (final bin now complete) |
| HAP-264 | Som.py support SomaticEVS feature for Strelka somatic |
| HAP-265 | Hap.py haplotype-matched TPs now assigned min qual from across the superlocus |
| Ticket | Description |
|---|---|
| HAP-248 | qfy.py fails when -V is not on |
| HAP-249 | stratification regions: include length of stratification region in *extended.csv |
| HAP-250 | stratification regions: allow to summarise performance by ID (4th column) |
| HAP-254 | Fix haploid GTs on chrX for male samples. |
| HAP-255 | support * alleles (and alleles that contain "*") to support octopus VCFs |
| HAP-256 | Sentieon caller extraction |
| HAP-257 | Fix PASS recall for complex matches |
| Ticket | Description |
|---|---|
| HAP-240 | Fix division by zero in som.py CI computation |
| HAP-241 | Add genotype validation to vcfcheck. Will now fail when alleles don't exist. |
| HAP-242 | Improved counts in bamstats.py |
| HAP-244 | Support the FT format field to enable per-sample filtering |
| Ticket | Description |
|---|---|
| HAP-232 | Fix help text in hap.py and pre.py |
| HAP-233 | INFO fields don't get mixed up in preprocessing anymore |
| HAP-234 | Forward unstructured headers through hap.py |
| HAP-236 | Fix quanitify test to work with compressed outputs |
| Ticket | Description |
|---|---|
| HAP-180 | Confidence intervals for precision and recall in som.py |
| HAP-221 | document how stratification region overlap is calculated |
| HAP-222 | document all output columns in result CSV files |
| HAP-223 | getFormatInt is broken / only returns DP, which leads to incorrect ROCs |
| HAP-225 | System BOOST install can break installation process. Only use included version. |
| HAP-226 | cnx gets wrong caller version for GATK in some cases |
| HAP-227 | QQ.Field should not be IQQ when using xcmp for comparison |
| HAP-229 | Hap.py fails when query does not contain all default chromosomes |
| HAP-230 | Compress large output files to save space when writing ROCs to JSON |
| Ticket | Description |
|---|---|
| HAP-175 | Enable GQX as a ROC feature |
| HAP-184 | check for empty query/ref vcf |
| HAP-185 | som.py --fix-chr-query does not fix MT appropriately |
| HAP-187 | som.py automatically resolve whether the --fix-chr-query switch is required |
| HAP-189 | refactor storage of INFO and FORMAT, extract preprocessing into separate script |
| HAP-192 | Missing chromosomes cause fp.rate computation to fail in som.py |
| HAP-197 | AF binning with arbitrary boundaries in som.py |
| HAP-201 | hap.py integration tests failing because of trailing white space |
| HAP-202 | F-score computation is not correct |
| HAP-204 | When no / wrong command line is specified, hap.py should have non-zero return code |
| HAP-205 | fix EVS feature support in som.py |
| HAP-206 | Fix header for BLT in hap.py output |
| HAP-207 | Count TP, FN and FP outside confident regions as UNK |
| HAP-208 | Simpler deployment with vcfeval |
| HAP-209 | Update documentation and release notes |
| HAP-210 | Calculate truth-QQ values as max over all query BS TPs |
| HAP-211 | Output BS in xcmp |
| HAP-212 | Improve ROC filter handling / add selective filtering |
| HAP-213 | Update Dockerfile |
| HAP-215 | include FDP in som.py indel features |
| HAP-217 | pad symbolic deletions in pre-processing for vcfeval |
| HAP-218 | improve pre.py command line usage |
| HAP-219 | Don't mix variants with different filtering during preprocessing |
| HAP-220 | Quantify counts hom-ref records as INDEL for UNK and for N |
| Ticket | Description |
|---|---|
| HAP-181 | Need documentation with detailed description of hap.py output |
| HAP-188 | Support GA4GH stratification regions |
| HAP-190 | Implement final output format for 0.3.0 |
| HAP-193 | Implement indel length binning |
| Ticket | Description |
|---|---|
| HAP-149 | Fix vcfeval integration via GA4GH interface |
| HAP-154 | ROC Support for Mutect2 |
| HAP-161 | Output GT precision and FP counts for wrong GTs and wrong alleles separately |
| HAP-166 | Indel haplotype enumeration bug |
| HAP-169 | Change quantify/xcmp output be GA4GH compliant |
| HAP-170 | Som.py ROCs not correct in some cases |
| HAP-171 | ROC support using vcfeval |
| HAP-176 | One run for PASS and ALL to fix ROCs |
| HAP-177 | CNX doesn't extract caller name correctly for Mutect2 |
| HAP-179 | Symmetric FP and FN for genotype mismatch |
| HAP-183 | Handling GATK gVCF <NON_REF> alleles |
| HAP-186 | Update documentation and release notes |
| Ticket | Description |
|---|---|
| HAP-147 | Normalisation problem where het-alts cancel each other out |
| HAP-151 | handle INDELs of undetermined length |
| HAP-152 | Implement Ti/Tv computation |
| HAP-155 | Improve support for GRC37 / non-chr-prefix references |
| HAP-157 | Calculate per-MB FP rate (as an "absolute" equivalent to precision)s |
| HAP-162 | Som.py outputs INF precision when FP and TP are 0 |
| HAP-163 | Release notes and final test |
| HAP-164 | Sync up som.py empirical scoring features |
| HAP-165 | Speed improvements in quantify and upgrade to htslib 1.3 |
| Ticket | Description |
|---|---|
| HAP-133 | Parse platypus version strings correctly |
| HAP-134 | Calculate AFs from BAM for som.py feature table |
| HAP-135 | Som.py labels some variants twice in admixture comparisons |
| HAP-136 | Better Strelka feature extraction |
| HAP-137 | GT ordering makes unit test fail |
| HAP-138 | Add het/hom ratio to output table |
| HAP-139 | Document hap.py in Docker usage |
| HAP-140 | Misleading error messages when checkout headers in hap.py |
| HAP-141 | Remove / improve reference check error message |
| HAP-142 | Som.py -- stratify by AF brackets |
| HAP-143 | Empty VCF files cause failure |
| HAP-144 | Add filtered FN vs. absent FN to result table |
| HAP-145 | Hap.py -o switch doesn't accept prefix in current directory |
| Ticket | Description |
|---|---|
| HAP-83 | premature exit when multimerging gvcfs |
| HAP-123 | Varscan2 DP rates are not calculated correctly |
| HAP-124 | Som.py --fix-chr-truth doesn't fix chr names in the ambi bed files |
| HAP-126 | Add VCF Validation Step |
| HAP-127 | Make -X the default behaviour (write extended metrics unless told otherwise) |
| HAP-128 | Hap.py ROCs for Freebayes and Platypus |
| HAP-129 | Som.py should support FP regions from Ambi file |
| Ticket | Description |
|---|---|
| HAP-119 | ROCs should use TP variant types from query, not truth |
| HAP-120 | Write ROC data into JSON output |
| HAP-122 | Integrate VCFEval for matching |
| HAP-121 | Installer fails on some systems |
| Ticket | Description |
|---|---|
| HAP-103 | Germline ROC curves |
| HAP-115 | --no-internal-* options are broken |
| HAP-116 | Quantify errors don't get printed |
| HAP-117 | Raw count quantify calls don't respect locations passed to hap.py |
| Ticket | Description |
|---|---|
| HAP-106 | blocksplit / quantify segfault when reading faulty VCF |
| HAP-107 | Som.py tests fail in SD |
| HAP-109 | Hap.py fails for ambiguous bases in reference fasta |
| HAP-111 | Remove muscle dependency code and legacy stuff that depends on it |
| HAP-112 | Add option for hap.py to disable haplotype matching |
| HAP-113 | Check for output folder at start |
| HAP-79 | Well-formed vcf output file |
| HAP-100 | Clean up tests, fix platform-dependent sorting issues |
| Ticket | Description |
|---|---|
| HAP-23 | Multi-sample variant graph implementation |
| HAP-52 | Create runner / wrapper script to run inside Docker |
| HAP-78 | Reference FASTA handling |
| HAP-88 | Refactor Cmake files to build included Boost, move build of dependencies to build folder |
| HAP-90 | Implement parallel graph enumeration |
| HAP-92 | Quantify should annotate the output VCF according to actual status |
| HAP-94 | Add allele counts by type (rather than per NT) back in |
| HAP-95 | Stratified feature output |
| HAP-96 | cnx aligners empty |
| HAP-97 | Hap.py does not quote or escape file path internally and fails on paths with spaces |
| HAP-99 | som.py should also be able to fix truth chr names |
| HAP-102 | Eliminate / clear up Locations.unknown |
| HAP-104 | Fix samtools build when using modules, add eb files |
| Ticket | Description |
|---|---|
| HAP-86 | Not all vcfeval sites are matched |
| HAP-87 | auto chr naming detection broken |
| HAP-89 | Treatment of filtered variants should not be as optional |
| HAP-93 | GT mismatches are not counted as FP when no confident regions are specified. |
| HAP-82 | Print error (or at least warning) for bogus command-line arguments |
| Ticket | Description |
|---|---|
| HAP-39 | Implement Allelic-primitive variant splitting |
| HAP-72 | QUAL misleading for type=missing records |
| HAP-74 | Remove setup.py |
| HAP-75 | Document the fact that bed files with tracks aren't supported. |
| HAP-76 | Add version information to output / simple output |
| HAP-77 | som.py should write puma metrics JSON file also |
| HAP-80 | Handle -P switch correctly for silver variants in PG 8.0 |
| HAP-81 | Support VQSR ROCs in som.py |
| HAP-84 | no hap.py versions in output |
| HAP-71 | Hap.py fails on BED files with track information |
| Ticket | Description |
|---|---|
| HAP-8 | Write user documentation |
| HAP-54 | Version number does not display |
| HAP-59 | Change som.py test to PG Admixture data |
| HAP-62 | hap.py non-verbose fail when FP regions file not found |
| HAP-63 | Add more comprehensive PG hap.py test (PGv7 vs. GATK 1.6 on chr21) |
| Ticket | Description |
|---|---|
| HAP-22 | Split ref-match blocks into SNPs and indels |
| HAP-44 | Clean up + Migrate Dockerfile to Ubuntu 14.04 |
| HAP-46 | Test + add GA4GH difficult indels to test set |
| HAP-49 | som.py should do ROC curves |
| HAP-56 | Define value in metrics.json |
| HAP-57 | -R option can make xcmp fail |
| HAP-58 | Add option for verbosity levels or to write message to log file |
| HAP-54 | Version number does not display |
| HAP-62 | hap.py non-verbose fail when FP regions file not found |
| HAP-63 | Add more comprehensive PG hap.py test (PGv7 vs. GATK 1.6 on chr21) |