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Release 1.4.0
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@nh13 nh13 released this 19 Oct 20:32
1.4.0
c2a8bd3

Important: Scala 2.12 cross-build support has been removed. (#614)

New tools in this release:

  • FixVcfPhaseSet: - Add a tool to fix the VcfPhaseSet (#612)

Updates to tools in this release:

  • SplitBam: Add an option to reduce memory usage if the input has many read groups (#622)
  • EstimatePoolingFractions: exclude sites at min coverage (#638)
  • EstimatePoolingFractions: use GT.AF for per-sample allele frequencies (#637)
  • MakeMixtureVcf: make more tolerant of fractions that don't add up to 1 because floating point math is hard with lots of samples. (#640)
  • GroupReadsByUmi: optionally allows inter-contig pairs (#648)
  • AnnotateBamWithUmis: Support a read structure for the FASTQ (#670)
  • TrimPrimers: can trim only R1s (#681)
  • CollectDuplexSeqMetrics: type in the usage (#691)
  • CollectDuplexSeqMetrics: add a plot for duplex yield (#692)
  • DemuxFastqs: remove the erroneous mention of --sample-sheet (#658)
  • CorrectUmis: add a cache (#702)
  • DemuxFastqs: Add an option to to insert sample barcodes in the FASTQ header (#711)
    • Added --omit-fastq-read-numbers to skip appending the trailing /1 and /2 to the output FASTQs.
    • Added --include-sample-barcodes-in-fastq to replace the last field in the first comment in the FASTQ header.
    • Added --illumina-file-names to name output FASTQs according to Illumina filename conventions
    • Deprecated --illumina-standards option in favor of the three options above
    • Added --platform option to specify the sequencing platform in the BAM read group header. Input FASTQ header must conform to Illumina standards when adding the sample barcode above
  • DemuxFastqs: Add an option to filter reads on the header filter flag (#713)
  • Added the option --omit-failing-reads to only output reads marked as passing in the FASTQ header comments. replaced with N's.
  • DemuxFastqs: Adding option to filter on the internal control flag, and accompanying tests (#714)
    • Added --omit-control-reads to omit any reads marked as control in the FASTQ read header comment.
  • DemuxFastqs: Add an option to mask bases below a specified quality threshold (#716)
    • Added --quality-threshold to specify a threshold to use for masking bases. Bases with a quality score below the threshold are
  • ErrorRateByReadPosition: Improve error message when no reference fasta .dict is provided (#728)
  • DemuxFastqs: Add metrics on base quality to the sample barcode metrics output (#720)
  • AnnotateBamWithUmis: Option to indicated sorted FASTQ to add UMIs more quickly (#729)

Updates to APIs in this release:

  • Updates to make the VCF api code considerably faster when reading VCFs with may samples (#609)
  • Have Metric classes correctly serialize EnumEntry fields to string (#601)
  • Add a brief description to AssignPrimersMetric (#616)
  • Support assembling JAR files with Java 11 (#645)
  • SampleSheet checks ID unique between samples with/without Lane (#684)
  • Log the last progress in Bams.queryGroupedIterator (#700)
  • Validate that a Variant and its Genotypes have the same alleles (#703)
  • Add "biotype" to Gene and update NcbiRefSeqParser to support more gene biotypes (#706)
  • Updates how NCBI RefSeq GFFs are parsed to enable parsing of genes that do not have canonical transcript entries below them (#706).
  • Add methods to make a Variant locatable (#699)
  • GenomicRange to support contig names with colons (#708)
  • Add helpers for mateCigar and matesOverlap on SamRecord (#717)
  • Resolve bug where empty string fields in Metric files would yield ':none:' values in the case class (#724).
  • Unify and add caching to the way Metric class names are accessed (#724)
  • Adding one more gene biotype for SRP_RNA. (#726)
Assets 3
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