167.3c5b8ae

What's Changed

• fix(qannotate): MIUN was not being applied appropriately to SNPs by @holmeso in #387
• Qsnp track unfiltered cs by @holmeso in #388
• perf(qbamfilter): minor speedups by @holmeso in #389

Full Changelog: 164.e3968a7...167.3c5b8ae

164.e3968a7

What's Changed

• Qcoverage fix by @newellf in #386

Full Changelog: 163.b34af16...164.e3968a7

163.b34af16

What's Changed

• perf(qmule:fastqtosamwithheaders): minor performance inmprovements by @holmeso in #377
• fix(qprofiler2): add ordering of readgroups in BamSummaryReport by @newellf in #378
• Qmotif revisit by @holmeso in #379
• Update qmotif_1_2.md by @holmeso in #380
• Update qmotif_1_2.md by @holmeso in #381
• Holmeso patch 1 by @holmeso in #382
• refactor(qcoverage): minor java21 refactoring based on IDEA suggestions by @newellf in #383
• perf(qpicard - cram): fork htsjdk to include performance enhancements for CRAM file reading by @holmeso in #384
• fix(qsv): fixing issue where references didn't match by @newellf in #385

Full Changelog: 155.f90a251...163.b34af16

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