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CHANGES.md

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CHANGES

5.7.4

  • Fix Dockerfile

5.7.3

  • Exit with a clearer error message when file does not pass the minimum read threshold
  • Update Dockerfile and setup.sh

5.7.2

  • OS and Bio::DB::HTS updates

5.7.1

  • Fixed bug that prevented vcf+bed locations being possible

5.7.0

  • Switch to low level HTS API to speed up fetch calls.
  • Collate mate read calls into single fetch for overlapping ranges.
  • ~46% faster - see #68.

5.6.1

  • Ensure line read rather than $_ are used in split
  • Update license years

5.6.0

5.5.0

  • Adds docker build - please use this in preference to other methods. Should be functional with singularity.

5.4.1

  • Remove help text about adding to allowed perl lib paths as not being used
    • corrected to indicate install skip for deps
  • Changed so that following are installed even when 'skip' is used
    • htslib/Bio::DB::HTS
    • vcftools
  • Removed hiding of errors during install
    • Some failures not surfaced so user needed to know to check $? or the setup.log file
  • Bio::DB::HTS requires current bioperl.

5.4.0

  • Reduced memory footprint for augment vcf file
  • Augmentation can now run per chromosome
  • SAM flag filters are now controlled by vafConstantas.pm file
  • .bas file now used by default to calculate library size
  • added support for cram files

5.3.9

  • Change max reads read when determining read length to 50k
  • Modify _get_bam_header_data to get the max read length of ALL bam files encountered and therefore to produce the correct lib_size
  • Converted internal SAM flag constants to point to Bio::DB::HTS constants (in the future internal constants could be replaced)
  • Added command line options for filter include and exclude of reads when checking read length
  • Added very simple test for _get_bam_header_data
  • All contribute to fixing #45
  • All hard tabs now spaces. Fixes whitespace part of #49

5.3.8

  • Updated CHANAGES.md with corerct version

5.3.7

  • corrected condition in vafcorrect for erroneous PASS flag setting

5.3.6

  • Correct query_full to ensure undef return is caught.
  • vaf output precison raised from two to four decimal places.

5.3.5

  • Update samtols and hstlib to v1.7
  • Update Bio::DB::HTS to v2.10
  • Change tabix->query call to tabix->query_full
  • fixed bug in accessing chr prefixed chromosome names for HDR regions

5.3.4

  • corrected typo in setup.sh removed safelist branches from .travis
  • Added checks for INST_METHOD
  • Changed CHANGES.md syntax to markdown linter
  • Exonerate install is now skipped if INST_METHOD is 2

5.3.2

  • Fixed bug which caused incorrent assignment of mutant reads overlapping deletion regions to Unknon category - if there is any mismatch in 3prime region from deletionstart site

5.2.2

  • Heade line for SAMPLE is now generated from command line
  • Fixed bug for missing header data when running with bedonly option

5.2.1

  • added condition to test vcf extension when bed file is not present

5.2.0

  • added functionality to process bed file per chromosome
  • progress file check during concatenation step ignores already processed chromosomes
  • vcf file extension is optional if --bedOnly option is selected

5.1.3

  • Fixed broken INFO tags in vcf and tsv
  • tags -t option is now only applicable to tsv file

5.1.2

  • forced default shell to bash for syste command

5.1.1

  • Added custom sorting for vcf files

5.1.0

  • User can now run per chromosome analysis [useful to run in parallel ] and concatenate the resulting files

5.0.0

  • Removed exonerate parameter to filter alignments based on score
  • Removed condition to discard alignment length smaller than read length
  • Added user defined option to specify exonerat percent value
  • Increased padding to extended reference sequence -- this will allow to map longer reads in amplicon data.

4.5.6

  • Update to Bio::DB::HTS install to use already installed htslib

4.5.5

  • updated version tag

4.5.4

  • Removed default high depth regions filter option, users can optionally provide this file on command line (refer wiki)

4.5.3 * Updated licensing policy

  • Added option to supply external ignore depth file
  • removed legacy code to run external commands
  • Added prerelease.sh to

4.5.2

  • Updated .gitignore to allow test data to be added to git

4.5.1

  • Updated test data set files

4.5.0

  • Added option to restrict reads based on mapping quality threshold

4.4.2

  • Exonerate --percent threshold reduced to 90 from 95 to allow 4 mismatches

4.4.1

  • More robust check for mismatches at varinat positions in the alignment

4.4.0

  • added additional condition to check mismatch at the variant region in the alignment
  • reads mapping on alternate sequence and have mismatch at variant region were categorised into UNK [ unknown ] reads
  • updated option to correctly read bed file

4.3.6

  • Creates augmented vcf file even if no records were augmented
  • Corrected processlog in vcf output header

4.3.5

  • Minor change to test script

4.3.4

  • Appropriate warning message when no vcf file found for a sample

4.3.3

  • updated changes.md and verision information

4.3.2

  • corrected tabix syntax as for Bio::DB::HTS::Tabix, added test for high depth region overlap

4.3.1

  • removed legacy script from Makefile

4.3.0

  • removed database dependecy code for external release

4.2.3

  • replaced Tabix with Bio::DB::HTS::Tabix

4.2.2

  • changed Bio::DB::HTS version to 1.12

4.2.1

  • changed Bio::DB::HTS version to 1.11

4.2.0

  • Added support to Bio::DB::HTS

4.1.17

  • Updated SQL query to get input data to generate commands

4.1.16

  • corrected condition to get unmatched normal

4.1.15

  • Fixed vcf header, as it was copied twice in the outfile

4.1.14

  • Added explicit check for normal sample using SIP_ATTRIBUTES table

4.1.13

  • updated defualt project ini folder to cgpVaf

4.1.12

  • Updated verison

4.1.11

  • Added condition to ignore writing progress file if augment only option is selected

4.1.10

  • Improved and corrected setup.sh and location of Makefile.PL

4.1.8

*added test to check final result removal *chnaged bio:db:sam version to 1.42

4.1.7

*changed installation path to bin from perl/bin in setup.sh

4.1.6

*fixed test to created progress file path

4.1.5

*updated condition to create outfile only if it is absent

4.1.4

*updated file postfix to _vaf

4.1.3

*Added tumour sample name as postfix to tmp folder

4.1.2

*Added setup.sh

4.1.1

*Fixed bug in unmapped mate retrival

4.1.0

*Added option to accept vcf file as command line input

4.0.1

  • Fixed readme file

4.0

  • Contains pre-calculated VAF values in FORMAT field
  • Per chromosome progress tracking i.e., failed jobs can be resumed from last unsuccessful chromosome
  • Added setup script script

3.2.4

  • Added condition to check snps that fall at the end of chromosome

3.2.3

  • Added option to create config file for user defined list of samples