inst/NEWS.md

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Changes in version 1.99.39 (2024-10-28) + Update in manuals. + Bug fix in .halfJoint() in estGeno().

Changes in version 1.99.34 (2024-10-19) + Minor fix in the coding in gbsrCalcProb.cpp in which a single ampersand was + replaced with double ampersands.

Changes in version 1.99.33 (2024-10-9) + Minor update in gbsrCalcProb() to offset too small genotype probability. + Minor update in estGeno() to allow users to explicitly specify whether to use + raw or filtered read counts for genotype estimation.

Changes in version 1.99.27 (2024-10-8) + Minor update in plotReadRatio(), plotDosage(), and getSamID() to include + parents in the plots as default. + Minor update in gbsrGDS2VCF() in which data nodes stored as "VL_Int" were + error prone and thus the code to remove VL_Int-type data was added. + A code to set data type to int64 for typical data that is converted to + VL_Int as default was added to gbsrVCF2GDS().

Changes in version 1.99.26 (2024-10-3) + Minor modifications in gbsrCalcProb.cpp and gbsrViterbi.cpp for a better + calculation speed. + Minor modification in setParents() to store parent sample information in the + GDS file. + Minor modification in gbsrGDS2CSV() to output estimated dosage data. + Minor bug fix in plotReadRatio(), plotDosage(), getGenotype(), and estGeno() + including .makeGenoParents().

Changes in version 1.99.17 (2024-9-25) + Modify the transition probability data structure (sparse matrix) to reduce + the data size. + Modify the offset setting to take a transition probability from the sparse + transition probability matrix.

Changes in version 1.99.16 (2024-9-12) + Update in the manuals and NAMESPACE. + Minor bug fix in plotDosage() and plotReadRatio().

Changes in version 1.99.14 (2024-9-9) + Update in the vignette.

Changes in version 1.99.13 (2024-8-29) + Replace set/getDominantMarkers() to set/getFixedBias().

Changes in version 1.99.12 (2024-8-28) + Minor bug fix in getGenotype(). + Modify getRead() and getGenotype() to make them work with the modified .filtData(). + Modify .filtData() because seqGetData does not work on polyploids. + Fix a bug in .summarizeEst() to support polyploids. + Fix a bug in .transitionProb() to support polyploids. + Update .getValidPat() and change the timing when .makePattern() run in estGeno().

Changes in version 1.99.3 (2024-8-27) + Fix bugs in the functions that have been modified to support polyploids. + Fix a minor bug in counting up chromosomes in .sumUpBias(). + Release of the developmental version of GBScleanR version 2. + GBScleanR version 2 supports polyploid populations.

Changes in version 1.9.22 (2024-8-27) + Update in gbsrGDS2VCF() to solve the issue that an open GDS file cannot be copied on Windows machines + Fix a minor bug in getGenotype().

Changes in version 1.9.20 (2024-6-11) + Version bump to sync the devel version and RELEASE_3_19. + Minor bug fix in getGenotype(). + Update README.

Changes in version 1.8.16 (2024-5-28) + Minor update in resetCallFilter().

Changes in version 1.8.14 (2024-5-23) + Minor update in setCallFilter().

Changes in version 1.8.13 (2024-5-22) + Fix a bug in setParents() with setting bi = TRUE.

Changes in version 1.8.10 (2024-5-21) + Fix minor bugs in closeGDS(), estGeno(), and the documents.

Changes in version 1.8.3 (2024-5-16) + Modify the estGeno() function to make it fix the parental genotypes at the + first half of markers, for the reverse-direction genotype estimation step, as + those were estimated in the forward-direction genotype estimation step. This + modification make the function to avoid estimating the different haplotype + combinations as the border of the first half and last half of markers after + the concatenation of the first half and last half of estimated haplotypes in + the .halfJoint() function.

Changes in version 1.8.2 (2024-5-16) + Update the vignette.

Changes in version 1.8.1 (2024-5-15) + Change .minimizeRecombination() to make it ignore the cases that are not listed + on the possible haplotype combinations. + Change the coding of .solveBorderConflict() to make it faster. + Add gbsrGDS2CSV() to output a CSV file. + Add setReplicates() to allow replicates in the data and modified estGeno() to + sum up read counts of replicates for genotype estimation. + Add makeScheme() to allow a simpler assignment of the scheme information.

Changes in version 1.5.13 (2023-10-17) + Update manual pages for plotDosage() and plotReadRatio().

Changes in version 1.5.11 (2023-10-2) + Fix a bug in setParents() that produces NA if a user set mono = TRUE and/or bi = TRUE.

Changes in version 1.5.8 (2023-8-14) + A user of GBScleanR reported the case in which there are NA values in read + count data in the AD node after conversion from a VCF file and results in a + fatal error during the genotype estimation process. + Since the VCF file that causes NA values in the AD node has not provided and + we have no clue to fix the bug in the data conversion, we tentatively added + the codes to set 0 to NA values in the read count data.

Changes in version 1.5.7 (2023-8-2) + Fix a bug in plotDosage() and plotReadRatio() where the selection of sample + ID had been wrongly conducted when sample filter have been set.

Changes in version 1.5.5 (2023-8-1) + Add a code to make EDS node in the given GDS after esetGeno() to store dosage information + when the given population is inbred biparental.

Changes in version 1.5.4 (2023-6-24) + Add an argument node in gbsrGDS2VCF() to switch genotype data to be output + into a VCF file. The setting node == cor replace data in the genotype node + of the given GDS file with the corrected genotype data stored in the + annotation/format/CGT node. + Add arguments info.import and fmt.import in gbsrVCF2GDS, and + info.export, fmt.export in gbsrGDS2VCF to specify the data to be + imported from a given VCF file or exported to a VCF file.

Changes in version 1.5.3 (2023-5-11) + Fix a bug in setInfoFilter() in which markers having no value for specified INFO + had been coded to be filtered out but now those can be retained.

Changes in version 1.4.2 (2023-4-26) + Fix a typo in a man page.

Changes in version 1.4.1 (2023-4-26) + Fix a bug in the vignette.

Changes in version 1.3.18 (2023-4-20) + Fix a bug in an example code in a manual page.

Changes in version 1.3.17 (2023-4-20) + Edit some codes to fit Bioconductor's requirements.

Changes in version 1.3.16 (2023-4-18) + Add the parentless mode in which estGeno() assign the number of dummy reads dummy_reads to dummy parents and estimate genotypes.

Changes in version 1.2.15 (2023-4-18) + Fix error found in build reports of Bioconductor

Changes in version 1.2.14 (2023-4-6) + Upon the request for multiple pedigree in the scheme, estGeno() supports a population consisting of samples that belongs to different pedigrees. + Deprecated the crosstype argument in initScheme(). + Add assignScheme() to let user specify which sample belongs to which pedigree.

Changes in version 1.2.9 (2023-2-14) + Minor change in genotype probability calculation algorithm which offset 0.5% when the minimum genotype probability is zero.

Changes in version 1.2.7 (2023-2-10) + Minor change in genotype probability calculation algorithm which set heterozygous calls impossible when the founders are inbred lines.

Changes in version 1.2.6 (2023-2-1) + Bug fix in HMM when a genotype is completely impossible to occur. + Bug fix in genotype pattern list for HMM when the pop is F1.

Changes in version 1.2.4 (2022-11-14) + Minor update in gbsrGDS2CSV().

Changes in version 1.2.3 (2022-11-14) + Bug fix in GBSR_HMM.cpp that caused a compile error in installation via bioconda.

Changes in version 1.2.1 (2022-11-11) + Minor modification in reference manual.

Changes in version 1.1.8 (2022-11-05) + Minor modification in gbsrGDS2CSV().

Changes in version 1.1.7 (2022-11-01) + Minor bug fix in gbsrGDS2CSV().

Changes in version 1.1.6 (2022-11-01) + Minor bug fix in gbsrGDS2CSV().

Changes in version 1.1.4 (2022-10-19) + Update in the refernece manual

Changes in version 1.1.4 (2022-10-19) + Minor bug fix in gbsrGDS2VCF().

Changes in version 1.1.3 (2022-10-19) + Minor bug fix in getRead().

Changes in version 1.1.2 (2022-10-19) + Fix a typo in the vignette

Changes in version 0.99.15 (2021-10-20) + Submitted to Bioconductor

Changes in version 0.99.16 (2021-10-20) + Fixed a bug that probabilities can be 0 for all genotypes when mismap rate is 1.

Changes in version 0.99.26 (2021-11-24) + Reformatted the scripts and the vignette to meet Bioconductor's instruction.

Changes in version 0.99.27 (2021-12-21) + Added detailed instruction for building a scheme object in the vignette.

Changes in version 0.99.28 (2021-12-21) + Added a code to close the file connection to GDS after opening file via + openGDS() called in the exmple section of the openGDS function.

Changes in version 0.99.29 (2021-12-23) + Fixed a bug in getRead() to get read counts of specified chromosome only. + Removed duplicated entries in Methods-GbsrGenotypeData.R.

Changes in version 0.99.30 (2022-1-15) + Fixed a bug in gbsrGDS2VCF(). + Reorganized cpp script.

Changes in version 0.99.31 (2022-2-14) + Reorganize scripts.

Changes in version 0.99.32 (2022-2-16) + Fix typo in gbsrGDS2VCF(). + Removed the test script for unused function.

Changes in version 0.99.33 (2022-2-16) + Reduced the example codes for the Scheme object.

Changes in version 0.99.34 (2022-2-24) + Fix a bug in getGenotype not to flip corrected genotypes.

Changes in version 0.99.35 (2022-3-16) + Fix a bug in the test script test_subset_n_gds2vcf.R.

Changes in version 0.99.36 (2022-3-18) + Add closeGDS(gds) at the end of sample script for gbsrGDS2CSV().

Changes in version 0.99.37 (2022-3-20) + No change, but just for version bump.

Changes in version 0.99.38 (2022-3-20) + Change the man page for gbsrGDS2CSV().

Changes in version 0.99.39 (2022-3-24) + Reorganized NAMESPACE.

Changes in version 0.99.40 (2022-4-25) + Fix a bug in plotReadRatio().

Changes in version 1.0.2 (2022-9-7) + Fix a bug in GBSR_HMM.cpp.

Changes in version 1.0.5 (2022-9-7) + Rewrote some scripts and replaced some function names for better user experience and code readability

Changes in version 1.0.6 (2022-10-17) + Rewrote vignette and reference manuals

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.