155.f90a251

What's Changed

• fix(qsv and q3tiledaligner): fix for GRCh38 by @newellf in #376

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

• feat(qmule): new classes for creating fastqs from BAMs and vice versa by @holmeso in #337

Full Changelog: 122.371bb21...123.cdccef6

122.371bb21

What's Changed

• qprofiler1 / qvisualise - handle new fastq header by @holmeso in #336

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