Releases: PlantandFoodResearch/MCHap
Releases · PlantandFoodResearch/MCHap
call-pedigree alpha 3
Beta v0.9.3
call-pedigree alpha 2
Alpha release of the call-pedigree tool (on top of version 0.9.3)
Beta v0.9.2
Bug Fixes:
- Avoid holding alignment file handles open #173
- Substantial reduction in memory usage and concurrent file handles
Beta v0.9.1
Beta 0.9.1
New Features:
- Allow complex sample pooling via the use of a tabular file
Beta v0.9.0
New Features:
- Added tool
mchap find-snvs
to generate a template VCF for assembly #166 - Option to report posterior probability of allele occurrence #162
- Added generic option to filter input haplotypes #168
Bug Fixes:
- Allow samples with multiple read groups #164
- Correct number of cores used when specifying multiple cores #150
- Simplify specification of prior allele frequencies #154
- Improve performance when working with CRAM files #167
CLI Changes:
- Added
mchap find-snvs
tool #166 - Added optional
--reference
argument to call and call-exact tools #167 - Replaced
--skip-rare-haplotypes
argument with--filter-input-haplotypes
#168 - Replaced
--haplotype-frequencies
and--haplotype-frequencies-prior
with--prior-frequencies
#154
VCF Changes:
- Added
AOP
field to record posterior probability of an allele occurring at any copy number #162
Internal Changes:
- Changes to using multiple process to minimize file handel creation #167
- Added
pandas
as a dependency
Beta v0.8.1
Bug Fixes:
- Fixed integer overflow bug when calculating the total number of unique haplotypes in mchap assemble #157
Internal Changes:
- Minor performance improvement to SNP homozygosity testing in mchap assemble
Beta v0.8.0
Beta v0.7.0
New Features:
- Mask reference allele when it is only reported to satisfy VCF spec #146
- Optionally report prior allele frequencies in
AFPRIOR
field - Filtering for some edge cases where genotypes should not be reported (
AF0
andNOA
)
Bug Fixes:
- Handle edge-case where all prior allele frequencies are zero #145
VCF Changes:
- Added
REFMASKED
info flag to indicate reference allele is amsked and should be ignored - Added
AFPRIOR
infor filed to indicate prior allele frequencies - Added
NOA
filter to indicate loci where no alleles were observed (e.g., masked reference only) - Added
AF0
filter to indicate invalid prior allele frequencies in which all frequencies were zero
Beta v0.6.0
New Features:
- Optionally output posterior allele frequencies #135
- Optionally specify a prior allele frequencies in
mchap call
andmchap call-exact
#120 - Optionally filter input haplotypes by input frequencies in
mchap call
andmchap call-exact
#113 - Improve PMF performance for
mchap call
andmchap call-exact
#125 - Allow pooling of all samples into single sample #140
- Allow arbitrary ploidy in PMFs #124
CLI Changes:
- Default to constant base error rate without using phred scores #127
- Replaced
--ignore-base-phred-scores
with--use-base-phred-scores
#127 - Increased default MCMC steps and burnin to 2000 and 1000 respectively #137
- Removed
--sample-list
argument #128 - Merged
--genotype-likelihoods
and--genotype-posteriors
into--report
#128 - Added option to report
AFP
via--report
#135 - Added
--sample-pool
argument #140 - Added
--haplotype-frequencies
parameter tomchap call
andmchap call-exact
- Added
--haplotype-frequencies-prior
flag tomchap call
andmchap call-exact
- Added
--skip-rare-haplotypes
parameter tomchap call
andmchap call-exact
- Removed
pedigraph
tool #138
VCF Changes: