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Published October 6, 2021 | Version 78.43982c9
Software Open

AdamaJava/adamajava: 78.43982c9

  • 1. QIMR Berghofer Medical Research Institute

Description

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

Files

AdamaJava/adamajava-78.43982c9.zip

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