version 0.7.3

Merge pull request #79 from JuseTiZ/master

[Enhancement] Add option to enforce reference allele consistency during liftover

version 0.7.0

1. Fix bugs for VCF file liftover.
2. Use "pyproject.toml" to replace “setup.py”.

v0.6.5

Fix these bugs when lifting over VCF files:

1. One of the alternative allele is "*" or other non-DNA characters.

version 0.6.4

1. Fix bug when the input bigwig file does not have coverage signal for some chromosomes.
2. When the input VCF file does not have CONTIG field, use long chromosome ID (e.g., "chr1") as default.

version 0.6.3

Fix bugs in v0.6.1. For insertions and deletions in a VCF file, the first nucleotide in REF and ALT fields correspond to the nucleotide at POS of the target reference genome

version 0.6.1

Same as version 0.6.0. Remove unused modules from the lib folder.

version 0.6.0

Major changes:

1. Use argparse instead of optparse.
2. Use os.path.getmtime instead of os.path.getctime to check the timestamps of fasta file and its index file.
3. Add ‘–unmap-file’ option to CrossMap.py bed command.

version 0.5.3

add "CrossMap.py viewchain" function
using builtin "logging" module
Fix bug in "CrossMap.py bigwig"

version 0.5.2

• In CrossMap.py region: keep additional columns (columns after the 3rd column) of the original BED file after conversion.
• Add ‘–no-comp-alleles’ flag to CrossMap.py vcf and CrossMap.py gvcf. If set, CrossMap does not check if the “reference allele” is different from the “alternative allele”.

version 0.5.0

Add "region" command to convert large genomic regions.