# Copy/Paste from https://data.broadinstitute.org/alkesgroup/Eagle/

Version 2.4.1 (November 18, 2018):
    Allowed --noImpMissing whenever input is provided in VCF format. (Previously, --noImpMissing was only allowed in reference mode when using 1 PBWT iteration.)
    Fixed bug causing --bpStart and --bpEnd to be ignored when --chrom was not specified. (Now --chrom is required with --bpStart/--bpEnd.)
    Added support for multithreaded HTSlib I/O (thanks to David Heise).
    Improved error-checking.
Version 2.4 (December 13, 2017):
    Fixed bug that had allowed target/ref allele flips: allele-matching was only being checked when --allowRefAltSwap was specified. Also enforced requirement that --allowRefAltSwap only apply to SNPs (not indels).
    Fixed bug causing a stack overflow for samples with very large numbers of missing genotypes (thanks to Laurent Francioli).
    Added --pbwtOnly option that skips non-PBWT iterations in non-reference mode (automatically set when N>200K).
    Added --keepMissingPloidyX option that keeps ploidy of missing VCF genotypes ('.' or './.') in chrX. (Because missing genotypes sometimes have incorrectly-coded ploidy, Eagle tries to guess the right ploidy by default.)
    Added --vcfExclude option for ignoring a list of variants when phasing in ref-mode.
    Allowed ‘chr’ prefixes in VCF chromosome names (to support hg38).
    Improved error-checking of genetic maps.
    Suppressed warnings about individuals with low heterozygosity when phasing chrX.
Version 2.3.5 (August 2, 2017): Fixed minor bug causing Eagle to erroneously terminate with failed assertion in rare cases.
Version 2.3.4 (June 5, 2017): Fixed bug causing incorrect imputation of missing genotypes prior to the first heterozygous site in each sample.
Version 2.3.3 (May 25, 2017):
    Fixed bug causing a crash when encountering all-haploid target sites in chrX.
    Fixed bug causing a crash when encountering sites polymorphic in only one of the reference or target (thanks to Petr Danecek).
Version 2.3.2 (March 23, 2017):
    Modified target/ref syncing to keep markers biallelic in the reference panel but monomorphic in the target data (via a change in htslib-1.4; thanks to Petr Danecek).
    Changed default VCF output format back to .vcf.gz (reverting accidental change in v2.3.1).
    Added genetic map for hg38 (lifted over from hg19).
    Added --outputUnphased flag to enable output of target-only sites (which are left unphased) when phasing using a reference.
Version 2.3.1 (March 3, 2017):
    Fixed bug causing rare crashes on samples with no hets.
    Fixed minor bugs in input reading.
    Improved error-checking and error-reporting.
Version 2.3 (July 22, 2016):
    Added support for phasing chrX (and added chrX genetic map).
    Optimized performance when phasing sequence data without a reference.
    Disallowed REF/ALT swaps for indels even with --allowRefAltSwap.
    Improved error-checking.
Version 2.2 (July 15, 2016):
    Added support for VCF/BCF input in non-reference mode.
    Reduced RAM when phasing sequence data in non-ref mode.
    Fixed bug causing crashes on samples with no hets.
    Fixed bug causing crashes on target hets monomorphic in the reference.
    Fixed other minor bugs. (Thanks to Stephan Ripke, Giulio Genovese, Christian Fuchsberger, and Sebastian Schoenherr for reporting bugs and assisting with debugging.)
Version 2.1 (July 6, 2016):
    Replaced in-sample imputation algorithm; new algorithm fills in missing genotypes during phasing (improving overall efficiency on sequence data).
    Added experimental --usePS parameter for specifying FORMAT:PS phase set constraints (--usePS=1 for soft constraint; --usePS=2 for harder constraint).
    Fixed minor error in recombination probability formula.
    Fixed minor bug (incorrect memset call) in first step of non-reference-based phasing algorithm.
    Fixed bug in input-checking (incorrect exit upon finding ”.” genotypes in target VCF).
Version 2.0.5 (May 26, 2016): Fixed bug in genetic map interpolation when using the --chrom flag.
Version 2.0.4 (May 24, 2016): Added error check for 0 Mb / 0 cM region span; added error check for memory allocation failures.
Version 2.0.3 (May 19, 2016): Added error check for 0 or 1 SNPs in intersection of target and ref.
Version 2.0.2 (May 19, 2016): Added --allowRefAltSwap flag to allow swapping of REF/ALT in target vs. ref VCF.
Version 2.0.1 (May 9, 2016): Fixed bug in region handling (thanks to Petr Danecek); added command line to VCF header.
Version 2.0 (May 3, 2016): Initial release of Eagle2.
Version 1.0 (September 23, 2015): Initial release of Eagle1.