bioforensics/MicroHapulator issues and pull requests

#189 - Compress intermediate FASTQ files

Pull Request - State: closed - Opened by standage 4 months ago

#188 - Compress intermediate sequence files

Issue - State: closed - Opened by standage 5 months ago

#187 - Fix test

Pull Request - State: closed - Opened by standage 5 months ago

#186 - New alerts in final report

Pull Request - State: closed - Opened by standage 5 months ago

#185 - Mark gaps instead of discarding

Pull Request - State: closed - Opened by standage 5 months ago

#184 - Additional warnings in report

Issue - State: closed - Opened by standage 5 months ago

#183 - Mark gaps instead of skipping

Issue - State: closed - Opened by standage 5 months ago

#182 - Replace BWA MEM with Minimap2

Pull Request - State: closed - Opened by standage 5 months ago

#181 - Enable a portable report directory

Pull Request - State: closed - Opened by standage 5 months ago

#180 - Report code refactor

Pull Request - State: closed - Opened by standage 7 months ago

#179 - HTML report sub templates attempt 2

Pull Request - State: closed - Opened by agshumate 8 months ago - 1 comment

#178 - HTML report sub templates

Pull Request - State: closed - Opened by agshumate 8 months ago

#177 - Clean up mapping stats in report

Pull Request - State: closed - Opened by standage 9 months ago

#176 - Make GRCh38 coordinates mandatory

Pull Request - State: closed - Opened by standage 9 months ago - 1 comment

#175 - Streamlining HTML report code

Pull Request - State: closed - Opened by standage 10 months ago - 2 comments

#174 - Change typing rate table to account for reads mapped to multiple markers at the same locus

Pull Request - State: closed - Opened by agshumate 10 months ago

#173 - Minimum read length filter

Pull Request - State: closed - Opened by agshumate 11 months ago

#172 - Sprucing up the report

Pull Request - State: closed - Opened by standage 11 months ago - 3 comments

#171 - Number of typed reads exceeding number of mapped reads

Issue - State: closed - Opened by agshumate 11 months ago - 1 comment

#170 - Suggested changes to filter-ambiguous

Pull Request - State: closed - Opened by standage 11 months ago - 2 comments

#169 - Add MultiQC plots to report

Pull Request - State: closed - Opened by agshumate 11 months ago

#168 - Replace donut plots with stacked bar graph

Pull Request - State: closed - Opened by standage 11 months ago - 4 comments

#167 - Ridge plots for read length distributions

Pull Request - State: closed - Opened by agshumate 11 months ago - 8 comments

#166 - InSilicoSeq verison 2.0

Issue - State: open - Opened by agshumate 12 months ago

#165 - Filter reads with too many Ns

Pull Request - State: closed - Opened by agshumate 12 months ago - 4 comments

#164 - Add initial N-filtering step

Issue - State: closed - Opened by standage about 1 year ago
Labels: enhancement

#163 - Repetitive read count fix

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

#162 - Trying to fix repetitive read counts

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

#161 - Add min length filter step after merging

Issue - State: closed - Opened by standage over 1 year ago

#160 - Improvements to QC visualizations in HTML report

Issue - State: closed - Opened by standage over 1 year ago

#159 - Updates for CI

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

#158 - Support multiple marker definitions at a single locus

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

#157 - Donut plots

Pull Request - State: closed - Opened by agshumate about 2 years ago - 3 comments

#156 - fixed numerical sorting on HTML report

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

#155 - Type-rate asc-desc table filter for percentages are not behaving correctly

Issue - State: closed - Opened by danejo3 over 2 years ago - 3 comments
Labels: bug

#154 - Dev installation command line instruction has type-o and `importlib-metadata` incompatible version number

Issue - State: open - Opened by danejo3 over 2 years ago - 2 comments

#153 - Make off-target analysis optional

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

#152 - Fix filter description in report

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

#151 - Add callplots, clean up marker detail HTML

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

#150 - removed base64 encoding for report

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

#149 - Add haplotype call plots to marker detail

Issue - State: closed - Opened by standage over 2 years ago
Labels: enhancement

#148 - Replace hard-coded filter thresholds in HTML report

Issue - State: closed - Opened by standage over 2 years ago
Labels: invalid

#147 - Implement single-end support for `mhpl8r pipe`

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

#146 - Per marker report

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

#145 - Perform variant calling at non-target positions

Issue - State: open - Opened by standage over 2 years ago - 2 comments
Labels: enhancement

#144 - Support single-end data in `mhpl8r pipe`

Issue - State: closed - Opened by standage over 2 years ago
Labels: enhancement

#143 - Off target mapping

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

#142 - Per-marker typing rate

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

#141 - Improve QC for off-target alignments

Issue - State: closed - Opened by standage over 2 years ago - 1 comment
Labels: enhancement

#140 - Conditional plotting of read length distributions vs. a summary table

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

#139 - Add different colors to report plots

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

#138 - HTML report color scheme

Issue - State: closed - Opened by standage over 2 years ago

#137 - Conditional plotting of read length histograms

Issue - State: closed - Opened by standage over 2 years ago
Labels: enhancement

#136 - Haplotype call plots

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

#135 - Draft: expose threshold parameters, produce interoperable profiles

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

#134 - Add support for custom targets in `mhpl8r pipe`

Issue - State: open - Opened by standage almost 3 years ago

#133 - Diagnostic messages

Issue - State: open - Opened by standage almost 3 years ago

#132 - Update documentation

Pull Request - State: closed - Opened by standage almost 3 years ago

#131 - Tweak plots

Pull Request - State: closed - Opened by standage almost 3 years ago

#130 - Add `mhpl8r getrefr` command

Pull Request - State: closed - Opened by standage almost 3 years ago - 3 comments

#129 - End-to-end microhap analysis pipeline

Pull Request - State: closed - Opened by standage almost 3 years ago - 6 comments

#128 - Plot read length distribution

Pull Request - State: closed - Opened by standage almost 3 years ago

#127 - New typing_rate method for TypingResult class

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

#126 - New API function / class method to compute aggregate and per-marker typing rate

Issue - State: closed - Opened by standage almost 3 years ago - 1 comment

#125 - New API function to compute and plot read length distribution

Issue - State: closed - Opened by standage almost 3 years ago - 1 comment

#124 - New command to grab hg38

Issue - State: closed - Opened by standage almost 3 years ago

#123 - Bugfix: markers with no valid reads (no coverage)

Pull Request - State: closed - Opened by standage almost 3 years ago

#122 - Heterozygote balance

Pull Request - State: closed - Opened by standage almost 3 years ago - 3 comments

#121 - Improvements to QA/QC for interlocus balance

Pull Request - State: closed - Opened by standage almost 3 years ago - 2 comments

#120 - Full analysis pipeline

Issue - State: closed - Opened by standage almost 3 years ago - 1 comment

#119 - Interlocus balance and heterzygote balance

Issue - State: closed - Opened by standage almost 3 years ago
Labels: enhancement

#118 - Add --reference flag for filter command

Issue - State: open - Opened by standage about 3 years ago

#117 - Fill out documentation

Pull Request - State: closed - Opened by standage about 3 years ago - 2 comments