CHANGELOG for QCTOOL:

** Version 1.4, released June 2014 **

* fix a bug with gzipped output that sometimes produced files with incorrect checksum.
* Fix crashing bug with Hardy-Weinberg P-value computation for large sample sizes (>45,000).

** Version 1.3, released September 2013 **

* A new option pair -[in|ex]cl-snps has been added. This reads a list of SNPs in the format output by the -write-snp-excl-list option. This is a file with 6 named columns, SNPID, rsid, chromosome, position, alleleA, alleleB.
* A bug preventing the -incl-snpids option from working correctly was fixed.

** Version 1.2, released June 2012 **

* Fix a bug handling VCF files with more than 10000 variants.
* Get line numbers right in errors relating to VCF files.
* Support bgzipped files via a tweak to boost (see boost TRAC ticket #6994 and #5904).
* Make -sort use temporary files in the same directory as the target (rather than a system directory.) This should improve its use on compute clusters.
* Support use of -sort with output .vcf files.
* New options -incl-positions and -excl-positions have been added.  Each takes a file containing a whitespace-separated list of genomic positions in the form chromosome:position.

** Version 1.1, released April 2012 **

New features:

* QCTOOL now has initial support for VCF files.
* New/renamed options for selection of SNPs: -[in|ex]clude-range, -[in|ex]cl-rsids, -[in|ex]cl-snpids, -[in|ex]cl-snps-matching.
	These replace -snp-excl-list, -snp-interval, and -snpid-filter.
	These are AND'd together to form the SNP filter, with the exception that repeated invocations of each -incl-X option are first
	combined.  Thus the command qctool -g example.gen -incl-range 06:25000000-40000000 11:0-10000000 -excl-rsids my_snps.txt
	will include all SNPs in either region that are not in the exclusion list.
* SNP filters which filter on SNP id fields (-[in|ex]clude-range, -[in|ex]cl-rsids, -[in|ex]cl-snpids, -[in|ex]cl-snps-matching)
    are now applied before the main qctool processing pipeline.  The practical consequence is that SNP exclusion lists written using
    -write-snp-excl-list do not contain the SNPs in any exclusion lists passed in.
* New option -condition-on, similar to SNPTEST's -condition_on, adds genotypic dosages to the output sample file.
* New -quantile-normalise option: quantile-normalisation of columns in the sample file.
* New -assume-chromosome option.  If this is used, QCTOOL will fill in missing chromosome values with the given one.
* New: support for multiple cohorts (by specifying -g and/or -s several times.)  SNPs are matched between cohorts using the fields
  specified by -snp-match-fields (which must include position).  If cohorts have the same alleles but they may be coded in opposite ways
	(e.g. cohort1 has "T C" and cohort2 has "C T"), use -match-alleles-to-cohort1 to flip the alleles appropriately.
* New option -sort, which sorts the output file.  Currently this works with BGEN, unzipped GEN, and unzipped VCF files.
* QCTOOL now writes a chromosome column in GEN file output by default.  This is understood by recent builds of SNPTEST but possibly not by other
    tools.  To suppress it, use -omit-chromosome.
* Change to the way the -snp-stats, -sample-stats, -write-sample-excl-list and -write-snp-excl-list options behave.
    Now each takes the name of a file to output, which must be specified.
* File output by -snp-stats has changed format slightly, removing the first column of numbers.
* QCTOOL no longer writes a log file by default: use -log to specify it.
* QCTOOL no longer has a default output sample file name.  You must specify -os whenever an output sample file is needed.
* QCTOOL now does not count lines in GEN or VCF files first.  This speeds up processing of large files.
* Fix bug where values in screen output are rounded to too low precision.

** Version 1.0, released 2008 **
- First release version.

