78.43982c9

New Features

• qsv: now using a tiled aligner rather than BLAT.

• qio: seven new package are created, which are extended from org.qcmg.record.RecordReader.

  • org.qcmg.tab is replaced by org.qcmg.qio.record.*, hence updated qsnp.
  • org.qcmg.illumina is replaced by org.qcmg.qio.illumina, hence updated signature.
  • org.qcmg.ma is replaced by org.qcmg.qio.ma, hence update qbamannotate , qprofiler.
  • org.qcmg.fast is replaced by org.qcmg.qio.fasta, hence update qprofiler.
  • org.qcmg.gff is replaced by org.qcmg.qio.gff, hence update qprofiler.
  • org.qcmg.gff3 is replaced by org.qcmg.qio.gff3, hence update qmaftools, qcoverage, qsv and qmule.
  • org.qcmg.vcf.VCFFileReader is replaced by org.qcmg.qio.vcf.VCFFileReader, hence update q3indle,qannotate.
  • org.qcmg.vcf.VCFFileWriter is replaced by org.qcmg.qio.record.RecordWriter, hence update q3panel, qpileup, qmule, q3vcftools, qprofiler, qprofiler2, qsignature, qsnp.
  • org.qcmg.gff3.gff3FileWriter is replaced by org.qcmg.qio.record.RecordWriter, at moment it is only used by qcoverage unit test.
  • org.qcmg.string.StringFileWriter is replaced by org.qcmg.qio.record.RecordWriter, at moment it is only used by qio unit test.

• qsignature:

  • snp positions file can now be a vcf file.
  • positions file can be streamed.
  • reporting upon positions listed within a gff3 file.
  • new class (VcfProfiler) to get info on vcf file produced by qsignature (such as WGS/WXS/panel etc)

Bug Fixes

• qvisualise: set message to the standard error output rather than null inside.
• q3tiledaligner: use synchronized map.
• qsv: check iSize value at begin of run.
• qcommon: VcfRecord toString method bug fix.
• qpileup: merge bug fixed and thread count set to 1

Other

• all tools: update unit test by using TemporaryFolder; org.junit.Assert to replace the deprecated junit.framework.Assert; deleting tests outputs, such as qprofiler.xml.
• qio, qcommon: move org.qcmg.pileup.QSnpRecord from qio to org.qcmg.common.model.QsnpRecord.
• qsnp: delete deprecated classes, they are TorrentPipeline, PileupPipeline, MuTectPipeline, BAMPileupUtil, QJumperWorker.
• qio: delete unused packages, they are org.qcmg.reader; org.qcmg.record; org.qcmg.primer*; org.qcmg.simple; org.qcmg.bed;org.qcmg.maf; org.qcmg.genesymbol; org.qcmg.consensuscalls; org.qcmg.Utils.
• qio: deprecate old packages which are only used by qmule, and qmule is dated and not maintained project. They are rg.qcmg.chrconv; org.qcmg.dbsnp; org.qcmg.pileup and org.qcmg.germlinedb.
• usage messages updated
• documentation updates

39.b903c82

New Features

• qio: new universal reader and writer classes to simplify io

Bug Fixes

• qannotate: don't add ALCAP fields by default.

Other

• qsv: reduce calls to SAMRecod.getReadGroup() as this is not a trivial operation
• q3tiledaligner: refactoring
• mkdocs: Final fixes for v1.0 of mkdocs documentation.
• qcommon: SmithWatermanGotoh moved here from qmule

32.eb889d9

In this release, a subfolder under root called "docs" is created. The documents for all adamajava projects are published there.

New Features
Bug Fixes
Other

• mkdocs: All paths are now relative to the docs directory NOT to mkdocs.yml
• mkdocs: Added Markdown docsi preparatory to hosting the docs on readthedocs.org.
• q3tiledaligner: renamned Q3TiledAligner to GenerateTiledAlignerFile
• qsv: renamed PairedEndRecord to ZPAnnotator
• Updated README.md

23.8546a7b

New Features

• Qprofiler2:
  • Read id information is reported for both FASTQ and bam mode;
  • Namespace is assigned in the schema file; qualification of elements and attributes are re-defined; universal attribute "schemaLocation" is used to indicate the schema file location.
  • The schema file is moved into subfolder V1 and V2 which is under the root folder, related md5 and release information is described its own readMe file.
  • Cram file is allowed as input with command-line input "-Dsamjdk.reference_fasta=/<path>/<reference.fa>"
• Qannotate: MIN flag now requires max(2, 3%) of reads in the normal, and MIUN flag now requires max(2, 3%) of reads in the normal.
• Qsv: some logging levels changed from INFO to DEBUG as log files are getting big.
• Qsnp: vcf mode no longer attempts to create compound snps from GATK vcf files. Instead, 2 (or more) individual snps are reported and qannotate will handle the case where qsnp calls a compound snp appropriately (ie. only evidence in qsnp will be required for a compound snp to be a PASS (assuming all other filters concur).

Bug Fixes

• Qprofiler2: error on readCounts in sequenceMetirc of FASTQ XML output, is fixed; attribute type is correct from "xs:integer "to "xs:long" or "xs:int" in schema file.
• Qannotate: Vcf2Maf had a bug whereby the tumour alleles were being inserted in to the matched normal alleles fields.
• Qsignature: deprecate unused compare class; output option is now correctly adhered to in SignatureGeneratorBespoke.
• Unit test under qSV, qpileup, qbasepileup are heavily changed due to the TemporaryFolder usage updating. The previous code won't work properly with the current junit-4.12.
• Q3TiledAligner: the class Q3TiledAligner is changed to GenerateTiledAlignerFile, it is more apparent.
• Qmotif: "OutOfMemoryErrors" issue is fixed.

Other

• The build file is upgraded from Gradle 2.14 to Gradle 6.4.
• The jar names no longer contain a version number. A jar files version will be dictated by the version of the parent (adamajava) folder.
• Google-style check is updated, now it allows variables name with single lowercase followed by uppercase; it allows single-line statements without braces.
• Bugs reported by spotBugs and styleCheck are fixed in some projects, eg. qcommon, qio, qprofiler2, qpicard.
• The readMe file is added into qmotif
• Q3 tools are merged into adamaJava including q3indel, q3vcftools, q3tiledaligner, q3panel.

7.a8ab31c.12803

New Features

• Qsnp overlap mode: overlapping reads (FFPE hello!) are filtered out.
• Qsv: added BGI (and MGI), novaseq, nextseq to list of approved platforms
• Qprofiler2: new tool
• Qsignature: new Compare class that will jointly compare vcf files generated by the traditional and newer bespoke methods.

Bug Fixes

• Qsv: fixed threading bug that came to light when dealing with lots of clipping
• Qannotate: chrM will remain as chrM rather than transforming into chrMT. Very useful when running against GRCh38, as it uses chrM.
• Vcf headers: add default values used to vcf header when applying filters
• Q3indel: fix vcf header so that it validates
• Vcf: GRCh38: fix sorting of vcf file entries so that they are in contiguous blocks, which allows them to be indexed
• Qannotate: fixed bug that caused make_valid mode to throw an ArrayIndexOutOfBounds exception. The fix invlolved updating qcommon's VcfMeta to handle sample names with underscores.

Other

• java threading classes have had their internal timeouts removed, or extended to 100 hrs to help combat the rising tide of super large BAM files
• move junit declaration to parent build file rather than individual project build files
• Updated main documentation to advise users that java 1.8 is required.
• Added README.md documentation to more projects
• removed sourceDependency=1.7 from qmaftools - it now picks up 1.8 from the parent build file

freeze qprofiler2 and qprofiler1

qprofiler2 have to freeze and release to outside; all tools here are compatible with GRCh37/hg19. Here we treat chrM as chrMT.

Paramaterise annotation process

Added options that allow the user to specify specific values used in the ConfidenceMode qannotate process. Reverted the HomozygousMode to behave as it did previously. More tests