Open Hub
Open Hub

 Settings |  Report Duplicate

1
I Use This!
Moderate Activity

Commits : Listings

Analyzed about 9 hours ago. based on code collected about 9 hours ago.
Aug 01, 2024 — Aug 01, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Add const to char *'s to ensure they can be called with fixed values without triggering compiler warnings
Martin Pollard
More... over 12 years ago
Import header comments from samtools
Martin Pollard
More... over 12 years ago
Use sizeof() and NULL instead of numbers
Martin Pollard
More... over 12 years ago
Fix crash on legacy files
Martin Pollard
More... over 12 years ago
vcffilter: Plot also bad sites in annotation distributions. Updated test files.
Petr Danecek
More... over 12 years ago
vcfquery: Enable -p option again
Petr Danecek
More... over 12 years ago
vcfisec: in the sites output mode print also file mask
Petr Danecek
More... over 12 years ago
vcffilter: check to prevent division by zero in the python plot script
Petr Danecek
More... over 12 years ago
gtcheck: fixed incorrect output, instead of uncertainty, the opposite (confidence) was reported before
Petr Danecek
More... over 12 years ago
vcfmerge: fix of copy-and-paste error in format field merging, use correct integer ranges
Petr Danecek
More... over 12 years ago
vcfgtcheck: Fix in INFO/DP parsing, wrong ID was used before
Petr Danecek
More... over 12 years ago
vcffilter: Plot also cropped annotation distributions to show the range of values actually used in filtering
Petr Danecek
More... over 12 years ago
vcfmerge: do not crash with non-overlapping chromosomes
Petr Danecek
More... over 12 years ago
vcfview: Restored the subset functionality (continued)
Petr Danecek
More... over 12 years ago
vcfview: Restored the subset functionality
Petr Danecek
More... over 12 years ago
vcffilter: plot annotation distributions
Petr Danecek
More... over 12 years ago
vcffilter: allow arbitrary order in -f and -l filtering options (X>value is same as value<X)
Petr Danecek
More... over 12 years ago
correct typos
Shane McCarthy
More... over 12 years ago
vcffilter: extended help message
Petr Danecek
More... over 12 years ago
bcf1_update_info fix: initialize bcf_info_t pointer, do not pass NULL
Petr Danecek
More... over 12 years ago
vcffilter: fixed a typo, output file names now named correcly based on filter type
Petr Danecek
More... over 12 years ago
vcfcheck: Do not run in streaming mode with the -t option
Petr Danecek
More... over 12 years ago
vcfcheck: complain if tabix index not available with -t option
Petr Danecek
More... over 12 years ago
vcfquery fix: Allow a mask file with the -v option
Petr Danecek
More... over 12 years ago
A few bugfixes from the previous two commits. New -S option in gtcheck and -H made work also in the cross-check mode
Petr Danecek
More... over 12 years ago
gtcheck: Removed forgotten debugging line
Petr Danecek
More... over 12 years ago
VCF/BCF core lib: Allow missing values in vectors. Note that this is a major change which, in contrast to BCFv2.1 specification, allows missing values in vectors. For integer types, the values 0x80, 0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001, 0x80000001 as end-of-vector indicators. Similarly for floats, the value of 0x7F800001 is interpreted as a missing value and 0x7F800002 as an end-of-vector indicator. This trial BCF version (v2.2) is compatible with the VCF specification and enables to handle correctly vectors with different ploidy in presence of missing values.
Petr Danecek
More... over 12 years ago
bgzip now compiles
Petr Danecek
More... over 12 years ago
vcfcheck: Do not crash at non-variant sites. Restore checking of two VCFs.
Petr Danecek
More... over 12 years ago
core vcf: added API for modifying/deleting/adding INFO fields, currently only VCF output supported; vcfmerge: AN,AC tags now updated correctly.
Petr Danecek
More... over 12 years ago