Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / gymreklab/TRTools issues and pull requests

#192 - Newtool mosaic str mgymrek

Pull Request - State: closed - Opened by gymreklab 12 months ago

#191 - Newtool mosaic str

Pull Request - State: open - Opened by LiterallyUniqueLogin about 1 year ago - 10 comments

#190 - mergeSTR vcf limit?

Issue - State: closed - Opened by aokulabasile about 1 year ago

#189 - Pato pena pato

Pull Request - State: closed - Opened by gymreklab about 1 year ago

#188 - Changed occurrences of mosaicSTR to prancSTR

Pull Request - State: closed - Opened by aarushi03 about 1 year ago - 1 comment

#187 - refactor: speed up for `TRRecord.GetLengthGenotypes()`

Pull Request - State: open - Opened by aryarm about 1 year ago

#186 - Updated the test files for mosaicSTR and simTR

Pull Request - State: closed - Opened by PatoPena about 1 year ago - 1 comment

#185 - dumpSTR is crashed to process the male chrX

Issue - State: open - Opened by weizhu365 about 1 year ago

#184 - refactor: use pysam instead of pybedtools

Pull Request - State: open - Opened by aryarm about 1 year ago

#183 - fix: vcf input via stdin

Pull Request - State: closed - Opened by aryarm about 1 year ago - 4 comments

#182 - mergeSTR can't merge haploid data from HipSTR output

Issue - State: open - Opened by Lidweixiang over 1 year ago - 2 comments

#181 - order of operations in dumpSTR

Issue - State: open - Opened by bioinfoYY over 1 year ago

#180 - Fix double allele mergeSTR bug

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 1 year ago

#179 - Conf change

Pull Request - State: closed - Opened by aarushi03 over 1 year ago

#178 - Logistic regression in AssociaTR

Issue - State: open - Opened by asuresh2 over 1 year ago

#177 - DumpSTR: Without --drop-filter, the output shows HET=-1 locus

Issue - State: open - Opened by Paddy1401 over 1 year ago - 1 comment

#176 - Fix a bug in qcSTR

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 1 year ago

#175 - Fix a docs bug

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 1 year ago

#174 - AssociaTR

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 1 year ago

#173 - Small update to the docs about Beagle

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 1 year ago

#172 - feat: encode TRs in PLINK2 PGEN files

Issue - State: closed - Opened by aryarm almost 2 years ago - 1 comment

#171 - Some questions about understanding the output of qcSTR

Issue - State: open - Opened by YiweiNiu almost 2 years ago

#170 - Add counting number of alleles to statSTR

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 2 years ago - 1 comment

#168 - Merge develop to master

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 2 years ago

#167 - Bring back support for GangSTR require support

Issue - State: open - Opened by gymreklab about 2 years ago

#166 - Delete requirements.txt.

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 2 years ago - 2 comments

#165 - Update PUBLISHING.rst

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 2 years ago - 1 comment

#164 - Add support for Beagle imputed VCFs

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 2 years ago - 4 comments

#163 - create_test_files.sh output warning

Issue - State: closed - Opened by yli091230 about 2 years ago - 1 comment

#162 - Feature request: run statSTR only on PASSing loci

Issue - State: open - Opened by gymreklab about 2 years ago

#161 - statSTR error when specifying samples on the command line

Issue - State: closed - Opened by gymreklab about 2 years ago - 1 comment

#160 - ValueError: Unexpected error. Stuck in infinite loop and exiting.

Issue - State: closed - Opened by jayala over 2 years ago - 2 comments

#159 - fix the minimum position bug in mergeutils

Pull Request - State: closed - Opened by yli091230 over 2 years ago - 2 comments

#158 - Bump numpy from 1.18.5 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#157 - IndexError: tuple index out of range

Issue - State: open - Opened by emersond368 over 2 years ago - 2 comments

#156 - Develop

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 2 years ago

#155 - Fixes in mergeSTR

Pull Request - State: closed - Opened by Kulivox over 2 years ago

#154 - compareSTR length genotype assumption

Issue - State: open - Opened by hopedisastro over 2 years ago

#153 - Merge str harmonization update

Pull Request - State: closed - Opened by Kulivox over 2 years ago - 1 comment

#152 - Bump numpy from 1.18.5 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#151 - Compare str comparison improvements

Pull Request - State: closed - Opened by Kulivox over 2 years ago - 2 comments

#150 - Fix one bug for mergeSTR with chrX

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 2 years ago

#149 - Bump to 4.0.2

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 2 years ago

#148 - mergeSTR does not output `GRID` info

Issue - State: closed - Opened by microtan0902 over 2 years ago - 1 comment

#147 - Hipstr flanking bp pos fix

Pull Request - State: closed - Opened by Kulivox over 2 years ago - 2 comments

#146 - [CompareSTR] Typo in condition and redundant condition

Issue - State: closed - Opened by Kulivox over 2 years ago - 1 comment

#145 - compareSTR compatibility with STR imputation results

Issue - State: closed - Opened by bibb over 2 years ago - 3 comments

#144 - Fix bug https://github.com/gymreklab/TRTools/issues/143

Pull Request - State: closed - Opened by LiterallyUniqueLogin almost 3 years ago - 1 comment

#143 - dumpSTR index error running HipSTR VCF output

Issue - State: closed - Opened by limrock1 almost 3 years ago - 4 comments

#142 - qcSTR TypeError when analyzing multiple samples

Issue - State: closed - Opened by MKBakker about 3 years ago - 2 comments

#141 - Update README.rst

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 3 years ago

#139 - Organize dockers

Issue - State: closed - Opened by gymreklab over 3 years ago

#138 - TypeError: vars() argument must have __dict__ attribute

Issue - State: open - Opened by psychrb over 3 years ago - 2 comments

#137 - reheader for mergeSTR?

Issue - State: closed - Opened by psychrb over 3 years ago - 6 comments

#136 - Numpy Error with dumpSTR

Issue - State: closed - Opened by alig99 over 3 years ago - 3 comments
Labels: bug

#135 - StatSTR sample subsetting

Pull Request - State: closed - Opened by gymreklab over 3 years ago

#134 - MergeSTR can now be run while trimming flanking alleles

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 3 years ago - 1 comment

#133 - Release 4.0.0 with cyvcf2!

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 3 years ago - 1 comment

#132 - Cyvcf2 mac tests

Pull Request - State: closed - Opened by nmmsv over 3 years ago - 1 comment

#131 - Trim flanking bps while merging

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 3 years ago

#130 - MergeSTR of adVNTR Files

Issue - State: closed - Opened by psychrb over 3 years ago - 8 comments

#129 - Document user-facing changes that have been made

Pull Request - State: closed - Opened by LiterallyUniqueLogin over 3 years ago

#128 - Cyvcf2 comparestr

Pull Request - State: closed - Opened by LiterallyUniqueLogin almost 4 years ago

#127 - Port mergeSTR to cyvcf2

Pull Request - State: closed - Opened by LiterallyUniqueLogin almost 4 years ago

#126 - Cyvcf2 dumpstr

Pull Request - State: closed - Opened by LiterallyUniqueLogin almost 4 years ago - 2 comments

#125 - Conflicting refs found at ****

Issue - State: closed - Opened by AhmedArslan almost 4 years ago - 2 comments

#124 - Adding BCFtools to docker file

Issue - State: closed - Opened by ambenj almost 4 years ago - 1 comment
Labels: enhancement

#123 - Adding citation info for the TRTools paper

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 1 comment

#122 - Cyvcf2 qcstr

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago

#121 - Because of a change a while back, the tools can no longer be run as s…

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 2 comments

#120 - Trying to fix set is not ordered errors

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 1 comment

#119 - Add a line saying we should make compareSTR more usable

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago

#118 - Update utils.py and statSTR to use cyvcf2

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago

#117 - Modify the tr_harmonizer to use cyvcf2 instead of pyvcf

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 3 comments

#116 - Trying to fix set is not ordered errors from Travis runs

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 2 comments

#115 - Xchrom

Pull Request - State: closed - Opened by ileenamitra about 4 years ago

#114 - adding missing GT FORMAT header line

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 1 comment

#113 - dumpSTR does not work for VCFs created using mergeSTR chrX

Issue - State: closed - Opened by ileenamitra about 4 years ago - 1 comment

#112 - dumpSTR: Set's loci Filter to "pass" incorrectly.

Issue - State: closed - Opened by ileenamitra about 4 years ago

#111 - upgrading docker to ubuntu 20.04

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 2 comments

#110 - StatSTR fixes and entropy statistic

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 4 comments

#109 - Fix docker installation issues do to install trtools improperly

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 2 comments

#108 - Dockerfix

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 2 comments

#107 - Dockerfile

Issue - State: closed - Opened by ileenamitra about 4 years ago - 5 comments

#106 - Allow bioconda builds to run commandline tests

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 1 comment

#105 - Some wording updates

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 1 comment

#104 - Release the changes

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 1 comment

#103 - plinkSTR issue: tool not working

Issue - State: closed - Opened by vishalrossi about 4 years ago - 1 comment

#102 - fixed HWE error for haploid

Pull Request - State: closed - Opened by ileenamitra about 4 years ago - 2 comments

#101 - Qc str fixes

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 8 comments

#100 - Updating main README + tool docstrings

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 2 comments

#99 - Adding command line testing to travis

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 1 comment

#98 - Add TRHarmonizer supplement to documentation. Clean up the docs layou…

Pull Request - State: closed - Opened by LiterallyUniqueLogin about 4 years ago - 1 comment

#97 - Adding Platinum Genomes Examples

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 7 comments

#96 - Updating info on supported genotypers

Pull Request - State: closed - Opened by gymreklab about 4 years ago - 4 comments

#95 - Adding example files and commands with Platinum Genomes trio for all supported tools

Pull Request - State: closed - Opened by gymreklab over 4 years ago - 2 comments

#93 - added message to reheader if contig info missing for mergeSTR

Pull Request - State: closed - Opened by gymreklab over 4 years ago - 3 comments

#92 - clarifying mergeSTR docs

Pull Request - State: closed - Opened by gymreklab over 4 years ago - 5 comments