2012-05-02 15:53  petr.danecek@sanger
    * vcf-consensus
    * vcf-indel-stats
    * vcf-compare: handle spaces in file names

2012-02-23 09:45  petr.danecek@sanger
    * vcf-merge: redundant ALT alleles are no longer removed by default but only with -t.
    * vcf-annotate: 
        - set the FILTER column, remove and annotate in one go (e.g. ID)
        - support of genotype columns in user filters
        - new --fill-type option

2012-01-23 10:41  petr.danecek@sanger
    * Notable changes since the last release:
        - fill-fs: new script for annotating VCFs with flanking sequence
        - fill-ref-md5: new script for annotating VCFs with 'reference' and 'contig' tags
            recommended by VCFv4.1
        - vcf-annotate: now also removes annotations and can apply user-defined filters
        - vcf-compare: changed output format, more stats reported and plots the results
        - vcf-fix-newlines: new script for fixing newline representation
        - vcf-phased-join: new script for joining pre-phased VCFs
        - vcf-query: significant speed up for some type of queries
        - vcf-sort: chromosomal ordering (1,2,10,MT,X rather than 1,10,2,MT,X) with new
            versions of unix sort
        - Vcf.pm: new set of API methods for faster access
        - some of the tools now work also with remote files 

2011-04-04 14:00  petr.danecek@sanger
    * VCFtools now support VCFv4.1
    * fill-ref-md5: New tool backfilling sequence MD5s into VCF header
    * Renamed merge-vcf, compare-vcf etc. to consistent naming vcf-merge, vcf-compare
    * vcf-merge: Now merging also GL and other Number=[AG] tags
    * vcf-compare: Comparing indel haplotypes

2011-02-21 12:31  petr.danecek@sanger
    * vcf-stats: new -s option to speed up parsing when stats computed for selected samples only
    * merge-vcf: allow to merge arbitrary chunks; -c option now deprecated, use -r instead
    * compare-vcf: change in output format and more detailed comparison

2011-02-17 17:36  petr.danecek@sanger
    * vcf-stats: allow querying stats of individual samples

2011-02-16 12:07  petr.danecek@sanger
    * vcf-stats: major revision
    * vcf-annotate: more filtering options

2011-02-04 14:43  petr
    * merge-vcf: if possible, calculate AC,AN even for sites without genotypes

2011-02-03 15:04  petr
    * merge-vcf: fixed a bug introduced by the previous fix.

2011-02-02 21:02  petr
    * merge-vcf: fixed a bug in merging indel ALTs. Only VCFs without samples were affected. 

2011-01-28 15:38  petr
    * vcf-subset: new option for printing rows with calls private to the subset group

2011-01-24 13:38  petr
    * Vcf.pm: uppercase floating point number expressions (such as
    1.0382033E-6) now pass validation

2011-01-20 08:28  petr
    * vcf-concat: print header also for empty VCFs with the -s option

2011-01-04 08:59  petr
    * vcf-isec, vcf-sort, Vcf.pm: replaced "zcat" by "gunzip -c"

2010-12-22 14:18  petr
    * vcf-annotate: New --SnpCluster option
    * Vcf.pm: new sub add_filter()

2010-12-15 13:44  petr
    * vcf-isec: By default output records from all files with unique positions
    (duplicate records from the same file still should be printed). With the -o
    switch, only positions from the left-most file will be printed.

2010-12-09 14:48  petr
    * query-vcf: Output 'True' for Flag tags when present and . when absent
    * vcf-annotate: Fix: the command line eats quotes when they are not escaped

2010-12-08 12:06  petr
    * Vcf.pm: throw an error when tabix fails.
    * query-vcf: enable streaming of files when region is not specified.

2010-12-02 11:53  petr
    * Vcf.pm: allow ALT alleles which are not present in samples
    * vcf-isec: Multiple files can be created simultaneously with all possible
    isec combinations. Suitable for Venn Diagram analysis.
    * merge-vcf: Do not remove ALT alleles if no samples are present
    * merge-vcf: Do FILTER merging more intelligently.
    * merge-vcf: Join the QUAL column: use average value weighted by the number of samples.

2010-11-28 08:34  petr
    * vcf-concat: Partial sort
    * vcf-validator: Added -u option
    * VcfStats.pm: dump_counts

2010-11-27 13:04  petr
    * vcf-subset: Filter variants by type

2010-11-26 09:08  petr
    * vcf-annotate: Added possibility to read header descriptions from a file

2010-11-24 13:25  petr
    * Fix in Vcf.pm:fill_ref_alt_mapping. VCF files processed with merge-vcf were
    affected when containing IDs in the ALT column.

2010-11-23 13:12  petr
    * Major revamp of Vcf.pm to allow better inheritance. Problems likely.