vcfnorm: New -b, --output-bcf option. Fixed a bug in realignment, indices i,j for ref,seq were reversed
vcfquery: Allow querying subfields of vectors via curly brackets
vcfcheck: New experimental indel stats - repeat consistency. Backup commit.
gtcheck: Reflected changes in HTSlib. Beware: Untested
vcfquery: Allow underscores in INFO/tag_name
Updated tests, cleaned the code to compile with the most recent HTSlib version.
Makefile: Added force target to redo version.h
Makefile: "echo -e" does not work on Mac OS, replaced by printf
Updated to the new regions/targets handling in synced reader. New -S option in vcfsubset.
Added new header file: bcftools.h
norm: Check status of fai_load call
vcfcheck renamed to vcfstats
view: Updated to renamed htslib macros; renamed -S option to -v
subset: Fix in the -i/e general filters
call: This is a backup commit. The multiallelic calling model is now working, but should be still considered experimental.
The "filter" command now for fixed-threshold filtering only; The original "filter" changed to "som"; Fixed broken "view" and "subset" shares the full-featured filtering with "filter"; Fixed memory leak in "stats"; Better ICB binomial test in "call" and DP4 annotation added; More tools now able to output both BCF and VCF and both can be compressed or uncompressed.
vcfcall: fix in ploidy initialization, do not assume mpileup gives the samples in the same order; fix in ref QUAL calculation
vcffilter,vcfnorm: added -o,-b switches
call: Prevent division by zero in calc_ICB
merge: Allow string types in FORMAT; Removed -b and replaced with -o switch