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CHANGELOG.md

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vcf2aln Change Log

Michael G. Campana & Jacob A. West-Roberts, 2017-2024
Smithsonian's National Zoo and Conservation Biology Institute
Contact: [email protected]

Version 0.13.2

Added --inferref option to infer reference when base is missing

Version 0.13.1

Fixed bug in reference-inclusion if missing sites are not skipped

Version 0.13.0

Added option to output reference sequence as part of the alignment

Version 0.12.1

Fixed glitch where the region ID was added to the sequence length value
Fixed glitch outputting a zero-length partition at beginning of table

Version 0.12.0

Added option to output contig partition table for concatenated alignments

Version 0.11.5

Handling for diploid missing data calls in haploid vcfs
encdoed-typo correction

Version 0.11.4

Fixed zlib requirement bug

Version 0.11.3

Now compatible with GATK deletions coded by *
Improvement to array summation

Version 0.11.2

Fixed bug when splitting regions by length that would cause misnumbering and overwriting of previous regions
Fixed bug for haploid data that did not properly count haploid missing data in the minimum calls filter

Version 0.11.1

Added method fix_name to resolve reserved characters in locus names

Version 0.11.0

Read/write gzipped files

Version 0.10.0

Probabilistic pseudohaplotype calling
Minimum samples called as a percentage option
Minimum alignment length to retain parameter

Version 0.9.0

Sample-specific filters no longer filter whole line
Completely filtered sites are excluded by the skip option
Renamed filters to better match standard tags

Version 0.8.0

--annotfilter option controls FILTER value filtration
--split_regions is now functional

Version 0.7.0

vcf2aln can read streamed uncompressed VCF
Removed extraneous debugging output from get_GT_tags

Version 0.6.0

get_GT_tags gets tag information from VCF rather than VCF 4.2 standard tags
Can read GATK HaplotypeCaller PGT phasing information
GT/PGT information do not need to be in first slot of output

Version 0.5.0

Speed increase using write-cycle controls
Indexing bug fix

Version 0.4.2

Haploid VCF bug fix

Version 0.4.1

Onehap bug fix

Version 0.4.0

Onehap concatenation bug fix

Version 0.3.0

Now gets all type fields in VCF
Onehap flag and bug fixes
GLE & ambiguity code handling
Cleaned up help screen

Version 0.2.0

New filters
Ability to identify VCF tags
Separation of methods

Version 0.1.0

Preliminary script to generate FASTA alignment from multi-sample VCF