Releases: AdamaJava/adamajava
Releases · AdamaJava/adamajava
155.f90a251
What's Changed
Full Changelog: 154.60ed31f...155.f90a251
154.60ed31f
What's Changed
- feat(qannotate confidence mode): allow the user to specify the homopolymer cutoff by @holmeso in #347
- refactor(qannotate nanno): use long to store chr and position by @holmeso in #348
- fix(qannotate): restore default value for HOM in confidence mode by @holmeso in #349
- fix(qsv): qsv can now write CRAM files internally by @holmeso in #350
- refactor(qcommon): minor java21 refactoring as advised by IDEA by @holmeso in #352
- fix(qprofiler): don't assume type of SAM attribute by @holmeso in #354
- Update BamSummaryReport.java by @holmeso in #355
- perf(adamajava): ensure code that calls SAMRecord.getReadGroup() does so sparingly by @holmeso in #356
- style(qmule): minor changes by @holmeso in #357
- Test branch felicity by @newellf in #358
- refactor: refactoring including removal of some unused parameters by @newellf in #359
- refactor: refactoring of qSV classes including those in util package by @newellf in #360
- refactor: minor java 21 refactoring of qsv packages by @newellf in #361
- Minor java21 refactoring based on IDEA suggestions for qsv by @newellf in #362
- refactor: minor java21 refactoring using IDEA suggestions for qsv tests by @newellf in #363
- Doco update by @holmeso in #365
- docs(fixed typo in comment): fixed typo in comment by @newellf in #366
- Qprofiler2 longread by @felicity731 in #368
- feat(qprofiler2 and qmule): adding isize and removing qname for qprof… by @felicity731 in #369
- fix(qbasepileup): chrM was automatically changed to chrMT by @newellf in #370
- refactor(qprofiler2): add bad option check for longread by @newellf in #371
- perf(qprofiler2): reduce calls to size on map by @holmeso in #372
- Qcoverage blacklist by @newellf in #373
- Qsv matefile by @newellf in #375
New Contributors
- @newellf made their first contribution in #358
- @felicity731 made their first contribution in #368
Full Changelog: 130.205fbf8...154.60ed31f
130.205fbf8
What's Changed
- qcoverage - change jaxb jars to prepare for newer java versions by @holmeso in #338
- feat(all projects): upgrade to java 21 by @holmeso in #339
- Update htsjdk to 4.0.2 by @holmeso in #340
- build(all projects): gradle updates, now works with vscode by @holmeso in #341
- fix(qannotate): snpeff records were not being dealt with correctly by @holmeso in #342
- fix(qsv): no jakarta bindings implementation available on classpath by @holmeso in #343
- explicitly call the JAXBContextFactory implementation class by @holmeso in #344
Full Changelog: 123.cdccef6...130.205fbf8
123.cdccef6
What's Changed
Full Changelog: 122.371bb21...123.cdccef6
122.371bb21
What's Changed
Full Changelog: 121.43a8f24...122.371bb21
121.43a8f24
What's Changed
- fix(qannotate:CCM) associate CCM.TWO with value 2 by @delocalizer in #335
Full Changelog: 120.d0f62cd...121.43a8f24
120.d0f62cd
What's Changed
- update SAMFileReaderFactory by @ChristinaXu2017 in #325
- update sam writer factory to cope with CRAM file by @ChristinaXu2017 in #327
- style(qcommon): addresses SpotBugs and some CheckStyle issues by @holmeso in #328
- New anno framework by @holmeso in #329
- qp2 kmers tweak by @holmeso in #331
- Set xml namespaceURI in ctor by @holmeso in #332
Full Changelog: 114.9838e15...120.d0f62cd
114.9838e15
What's Changed
- fix(q3tiledaligner): bug in comparator caused IllegalArgumentException by @holmeso in #326
- fix(qcommon:blatrecord): compareTo() throws NPE if qname is null by @holmeso in #326
- refactor(qcommon:blatrecord): wrong StringUtils class being by @holmeso in #326
Full Changelog: 113.f41ab39...114.9838e15
113.f41ab39
What's Changed
- create tool to rescue fastq reads with empty sequence by @ChristinaXu2017 in #321
- close writer by @ChristinaXu2017 in #322
- feat(qsignature): add gene model information to snp positions vcf file by @holmeso in #323
Full Changelog: 110.a2ced6c...113.f41ab39
110.a2ced6c
What's Changed
- update picard version by @ChristinaXu2017 in #282
- Qsamtofastq by @ChristinaXu2017 in #283
- update document for qmule by @ChristinaXu2017 in #284
- Qsignature Compare - handle empty vcf files by @holmeso in #285
- add exception message to log file by @ChristinaXu2017 in #286
- update log message for qmule::QSamToFastq by @ChristinaXu2017 in #287
- create new qsv document by @ChristinaXu2017 in #268
- create new qpileup document by @ChristinaXu2017 in #274
- Qprofiler2.doc by @ChristinaXu2017 in #288
- Qsignature - use cutoffs specified in options by @holmeso in #291
- qp2 - use s3 aware reader by @holmeso in #290
- remove class loading by @holmeso in #293
- Update import order in google_check.xml by @holmeso in #292
- qsignature cleanup by @holmeso in #295
- check isPresent before calling get on Optional by @holmeso in #299
- q3tiled_aligner cleanup by @holmeso in #300
- tidy up qmito by @ChristinaXu2017 in #297
- q3indel cleanup by @holmeso in #296
- continue on qmito.doc by @ChristinaXu2017 in #301
- tidy up qcoverage by @ChristinaXu2017 in #294
- fix bug in qpileup view mode by @ChristinaXu2017 in #302
- Q3ta options by @holmeso in #308
- build(all): update htsjdk jar from 2.14.1 to 2.24.1 by @holmeso in #310
- Qpileup.view.bug by @ChristinaXu2017 in #309
- update document on qbasepileup by @ChristinaXu2017 in #311
- fix(q3tiledaligner): remove dependence on GRCh37 by @holmeso in #313
- fix(qsv): incorrect index value was being passed to method by @holmeso in #314
- Qsv q3ta bug fix by @holmeso in #315
- refactor(q3tiled_aligner): allow user to pass in cached ref index map by @holmeso in #316
- feat(qsv): use ref index to determine positions by @holmeso in #319
- update MODE:add header line in remove mode by @ChristinaXu2017 in #320
Full Changelog: 78.43982c9...110.a2ced6c