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CHANGES

3.5.7

  • Update to discarded variant script to allow sorting of vcf discarded variant file

3.5.6

  • Adding parameters to "bcftools mpileup" call to resolve issue for samples using multiple wells
  • Correcting code version

3.5.5

  • Fix bugs in nanoseq result plotter
  • Fix bugs in indel caller

3.5.4

  • Fix bugs in nanoseq result plotter

3.5.3

  • Fix bugs in nanoseq result plotter

3.5.2

  • Remove non-deterministic behaviour from indel caller
  • Missing semicolon in snv_merge_and_vaf_calc.R

3.5.1

  • Dockerfile updated to avoid snv_merge_and_vaf_calc.R bug and to improve reproducibility
  • Small change to hardcoded overlapping_mask value in indel caller

3.5.0

  • Minor bug in the indel pipeline fixed (was using bitwise OR instead of logical OR)
  • New quality metrics added to the indel calls such that SNVs and indels come out with the same metrics

3.4.0

  • Fixed faulty PART step that was dropping last genomic intervals for targeted experiments
  • Refactored how indels get merged to avoid errors when scaling up calculations
  • Updated htslibs, samtools, bcftools and libdeflate

3.3.0

  • Added new INFO fileds to the final vcf
  • Changes to indel calling to reduce false calls
  • Added burdens output to nanoseq plotter
  • Fixed bugs in the VAF script

3.2.1

  • Fixed bug in part with empty intervals at end of genome

3.2.0

  • Modified BAM processing as to keep unmapped reads
  • Fixed VCF filter bug in VAF script

3.1.0

  • Fixed type error of VAF script

3.0.0

  • Made changes to accomodate targeted NanoSeq

2.3.3

  • Added quotes add various places to support ant chromosomes
  • Fixed error with 1 bp intervals
  • Fixed efficiency calculation problem with coordinates outside of chr ends

2.3.2

  • Reverted to old efficiency calculation

2.3.1

  • Added safe creation of tmp dir
  • Re-read input file to reduce mem usage in efficiency calculation

2.3.0

  • Cleaned up/ simplified variantcaller.R
  • Added extra check for turncated dsa output

2.2.0

  • Tested with targeted data
  • Fixed issue with coverage done files
  • Fixed bamcov so that it handles chromosomes without coverage
  • Fixed required/optional arguments from docustring
  • Fixed incorrect default argument (-d)
  • Added argument for file name of results
  • Removed plugin option from htslib that was causing issues with CRAM
  • Set seqs_per_slice to 1000 in htslib for improved CRAM streaming
  • Fixed off by one errors in part
  • Fixed interval test in part
  • Added consistency checks for contigs in BAM files

2.1.0

  • Added CRAM support
  • Fixed issue with sort in indel pipeline

2.0.0

  • Fixed 1-off error in dsa code.
  • Incorporated Indel scripts.
  • Incorporated new code for quick coverage estimation.
  • Rewrote Python wrapper.
  • Updated licenses.

1.5.3

  • Fixed bug with last interval for outlier case

1.5.1

  • Added more error captures for htslib calls

1.5.0

  • Updated R library installation script
  • Added option to skip post processing step
  • Simplified excluded chromosome option
  • Reduced default coverage window

1.4.0

  • Initial public release
  • Updated to htslib 1.11
  • Added licencing information
  • Added error checks when reading