vcfhacks Activity
simple to use commandline programs for VCF filtering and manipulation
Status: Alpha
Brought to you by:
gantzgraf
Activity for vcfhacks
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David Parry committed [6056ad]
update bianries
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Dave committed [7b32a2]
add binary and script specific readmes
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improve efficiency of new sort sub
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include Sort::External. Cleanup binary folder w...
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mac specific problems
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move vep plugins to own folder
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add binary info
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improve efficiency even more (maybe?) if contig...
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formatting
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add linux binaries
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delete binaries and relocated modules
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Merge branch 'master' of https://github.com/gan...
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add mac os x binaries
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fix issues with External::Sort
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use pp5.16 on mac os x and refactor pod2usage t...
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add space after SYNOPSIS heading so that Pod::U...
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add space after SYNOPSIS heading so that Pod::U...
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move vep plugins to own folder
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move doc to end of file
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add make binaries script
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update mac binaries to fix entrezgene.pm problems
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remove double pipes in place of or
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Merge branch 'master' of https://github.com/gan...
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Merge branch 'master' of https://github.com/gan...
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rebuild binaries so that pod works
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Merge branch 'master' of https://github.com/gan...
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correct filesize check
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add linux par file (perl v 5.14.2)
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add macosx par (perl 5.16.3)
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correct error with gene_id_mode option spec
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update readme files for new release
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correct processing of VEP alleles when SNV/MNV ...
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use pod2usage on failed GetOptions
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add make_par.pl script
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add relevant readme/examples files
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corrections to module loading when creating PAR
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remove outdated references to modules
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improve in memory sort functions and correct bu...
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add utilities for making disitributable scripts...
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vcfhacks released /vcfhacks/vcfhacks_v0.1.17.tar.bz2
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fix stray printing of message to STDOUT
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change INFO line to conform to VCF header spec
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add link to ensAnnotatorDb on github
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added v0.1.6 release notes to readme.md
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fix two incorrect regexes checking for .gz exte...
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support RefSeq/Entrez genes in addition to Ense...
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add --progress option, do not include gene2refs...
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remove rtf examples, add emphasis to examples.md
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add lib folder information
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add link to examples markdown document
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use lib folder for perl modules for sake of tid...
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make it clear that we need to use the same buil...
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updated examples
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only get GQ field once and store it for _getGen...
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fix unnecessary attempt to split REF field (REF...
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allow for VEPs inconsistant representation of i...
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check whether --quality ($min_qual) is true bef...
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remove erroneous references to gmaf in pod and ...
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fix extra column problem when using --summarise...
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add support for SnpEff annotations
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allow use of gene ID annotations for --list gen...
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remove redundant hash variable
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tidy code, improve allele handling
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fix duplicate lines for different matching tran...
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write biallelic sample information to INFO field
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fix duplicate lines for different matching tran...
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make INFO tag specific to findBiallelicVep to d...
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fix duplicate lines
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write biallelic samples to INFO field
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version 0.1.15 update
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added --contains_variant option to summarise sa...
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correct the split variant flag
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make sure we have defined fields before checkin...
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clarify in output when we cannot find a canonic...
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multiple changes to database update workflow
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documentation improvements
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fix numbering of files for progress when updati...
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use COMMON tags if available
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fixed problem with generifs and MGI data. Updat...
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fixed missing generifs and MGI phenotypes
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allow suppression of warnings from getVepFields
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make sure we chomp header when checking samples
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check "file" key is defined when parsing database
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only check for identical samples on first pass ...
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added markdown version of examples
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add LICENSE.txt
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for sortVcf method do not replace header if obt...
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add gpl.txt to repo
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sortVcf method supports addition/replacement of...
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code blocks
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added option to provide a sequence dictionary t...
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