Make nucleotide tables const
Amend .gitignore to ignore produced binaries
Cumulative commit with many changes, including:
- symlinking htscmd enables abbreviated commands
- header manipulation routines in htslib/vcf.*
- test suite for checking consistency
- improvements and new features in existing vcf*commands
- skeleton of vcfmerge (not fully functional yet)
- bugfixes
Bug fix: variant type not checked in the absence of --collapse option, this affected all vcf* commands
Changed order of underscore escaping and line breaking to prevent loss of escape characters
In calc_ac check added for different BCF_BT_INT* types; New trim_alleles method
Fix in variant type recognition: distinguish indels from complex events
Plotting Hets vs Homs instead of plain Hets; Sanity check for FS section header
Add missing contigs to the header permanently
Removed repeated call of bcf_unpack_fmt_core in vcf_format1
New API routine: remove_alleles; get_fmt_ptr
New API routine: remove_alleles; get_fmt_ptr
New API routine: remove_alleles; get_fmt_ptr
Do not attempt to read directories in bcf_sr_set_samples
Use uint64_t for DP stats. On behalf of Chris: plot-vcfcheck can now merge per-chromosome vcfcheck files.
Fixed a typo which rendered -n <cnt> ineffective.
New -C, --complement option for vcfisec. bcf_seqnames now returns chromosomes in correct order
Temporary changes
tmp save
GT merging now functional