Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / broadinstitute/longbow issues and pull requests
#208 - Issues with 'annotate' and 16-element arrays
Issue -
State: open - Opened by hdm-23 12 months ago
#207 - ModuleNotFoundError: No module named 'ordered_set'
Issue -
State: open - Opened by xuxia10 12 months ago
- 1 comment
#206 - Installation conundrum
Issue -
State: closed - Opened by phpeters about 1 year ago
- 2 comments
#205 - TypeError: create_simple_split_array_element() missing 1 required positional argument: 'split_read_index'
Issue -
State: closed - Opened by ashokpatowary over 1 year ago
#204 - rebuild HMM inside subprocesses
Pull Request -
State: closed - Opened by jamestwebber over 1 year ago
#203 - moved load_model to allow stream processing
Pull Request -
State: open - Opened by jamestwebber over 1 year ago
#202 - Updated python version
Pull Request -
State: open - Opened by jamestwebber over 1 year ago
#201 - allow "longbow inspect" from file of read names
Pull Request -
State: open - Opened by jamestwebber over 1 year ago
#200 - move models to JSON files
Pull Request -
State: open - Opened by jamestwebber over 1 year ago
- 1 comment
#199 - pysam output issue
Issue -
State: open - Opened by voyn over 1 year ago
- 4 comments
#198 - removed unused imports, fixed f-strings, etc
Pull Request -
State: closed - Opened by jamestwebber over 1 year ago
#197 - stream read less than specified amount, expected 4, found 0
Issue -
State: open - Opened by TinyTasy over 1 year ago
- 2 comments
#196 - Some minor fixes
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#195 - New documentation on custom Longbow models.
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#194 - Kvg mas16
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#193 - Can Longbow segment libraries using alternatives to the 10X 5' and 3' sequences?
Issue -
State: closed - Opened by claumer almost 2 years ago
- 2 comments
#192 - let inspect command read from stdin
Pull Request -
State: closed - Opened by jamestwebber almost 2 years ago
- 1 comment
#191 - Confusion over longbow correct
Issue -
State: closed - Opened by sagnikbanerjee15 almost 2 years ago
- 2 comments
#190 - random segment extraction no longer an option?
Issue -
State: open - Opened by morellr almost 2 years ago
- 1 comment
#189 - Fixing a bug that caused `correct_umi` to fail on unaligned bams.
Pull Request -
State: closed - Opened by jonn-smith almost 2 years ago
#188 - Exposed the back alignment score parameter in `correct_umi`
Pull Request -
State: closed - Opened by jonn-smith almost 2 years ago
#187 - How to get barcode and umi file after extract step ?
Issue -
State: closed - Opened by hmyh1202 almost 2 years ago
- 2 comments
#186 - Fixed all potential divide by 0 errors in logging.
Pull Request -
State: closed - Opened by jonn-smith almost 2 years ago
#185 - Updated `correct_umi` with some additional features.
Pull Request -
State: closed - Opened by jonn-smith almost 2 years ago
#184 - Exposed more `correct_umi` parameters
Pull Request -
State: closed - Opened by jonn-smith almost 2 years ago
#183 - get_segments(...) now returns three things rather than two
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#182 - Add a pseudocount for num_reads to prevent a rare divide-by-zero error
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#181 - Fix parsing of zero-length segments
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#180 - Fixed bug with collapse annotations wherein the length of the first a…
Pull Request -
State: closed - Opened by kvg almost 2 years ago
- 1 comment
#179 - Kvg minor fixes for sim
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#178 - `tagfix` does not update the cigar tag
Issue -
State: open - Opened by jonn-smith almost 2 years ago
Labels: bug
#177 - New segment cigars need to be refactored
Issue -
State: open - Opened by jonn-smith almost 2 years ago
Labels: bug
#176 - `models --dump` graph `png` output needs a better layout algorithm.
Issue -
State: open - Opened by jonn-smith almost 2 years ago
Labels: enhancement, good first issue
#175 - New `models` command no longer dumps all file formats of models to disk.
Issue -
State: open - Opened by jonn-smith almost 2 years ago
Labels: bug, High Priority
#174 - Move to `.sam` files for all test data
Issue -
State: open - Opened by jonn-smith almost 2 years ago
Labels: good first issue, tests
#173 - Kvg hierarchical models
Pull Request -
State: closed - Opened by kvg almost 2 years ago
#172 - Added `umi_correct` tool.
Pull Request -
State: closed - Opened by jonn-smith almost 2 years ago
#171 - `XQ` tag has an off-by-one error in its calculations
Issue -
State: open - Opened by jonn-smith almost 2 years ago
Labels: bug
#170 - documentation on how to create new models
Issue -
State: open - Opened by krobison13 about 2 years ago
- 2 comments
#169 - bump python req
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
#168 - pass bam header as dict for subprocesses
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
#167 - fix syntaxwarning in python 3.8: `is not ""` is not recommended
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
- 1 comment
#166 - bump python requirement to <3.8
Issue -
State: closed - Opened by jamestwebber about 2 years ago
- 3 comments
#165 - Refactor tests to be more independent
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
#164 - We need to store the segments that `sift` generates in a new tag in the reads (NOT the `sg` tag).
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: High Priority
#163 - fixed various bugs and tests
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
#162 - Add warning to `correct` if the user is using more than 1 thread.
Issue -
State: open - Opened by jonn-smith about 2 years ago
#161 - 3' model UMI should be changed to 12 bases for latest 10x kits
Issue -
State: closed - Opened by jonn-smith about 2 years ago
- 2 comments
Labels: High Priority
#160 - Fixed 10x3p model UMI length and added extra progress printing
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#159 - tweaked how subcommands were added at runtime
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
#158 - fixes/updates for setup
Pull Request -
State: closed - Opened by jamestwebber about 2 years ago
#157 - longbow correct consumes very large amount of memory
Issue -
State: closed - Opened by sagnikbanerjee15 about 2 years ago
- 1 comment
#156 - help. For the CD8 datasets
Issue -
State: closed - Opened by hmyh1202 about 2 years ago
- 1 comment
#155 - Fix PyPi failures
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: bug, High Priority
#154 - Fixed issue with tags in reads passed through the `sift` command
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#153 - Must add `sift` step to `longbow stats`
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: enhancement
#152 - Replaced `pomegranate` with fork that fixes heap overflow for long, repetitive reads.
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#151 - Added read ignore list option to `sift`
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#150 - `Sift` tool must be updated to work for arbitrary models / libraries
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: enhancement, High Priority
#149 - Filter out non-conforming cDNA molecules and write some stats on how they fail the filter.
Pull Request -
State: closed - Opened by kvg about 2 years ago
#148 - Now segment model quality tag (XQ) is segmented along with the SG tag.
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#147 - Review `pyro` and newest version of `pomegranate` for HMM improvements
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: enhancement
#146 - `segment` UMI/CBC filtering is currently broken
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: bug
#145 - The `XQ` tag must be truncated during `segment`
Issue -
State: closed - Opened by jonn-smith about 2 years ago
- 1 comment
Labels: bug
#144 - Added `tagfix` command to correct position tags post-alignment.
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#143 - Splitting the segmented bam file?
Issue -
State: open - Opened by ashokpatowary about 2 years ago
- 8 comments
Labels: enhancement
#142 - Add `barcode-peek` command to identify which barcode list to use
Issue -
State: open - Opened by jonn-smith about 2 years ago
Labels: enhancement
#141 - Fixed issues in `segment` with bulk libraries.
Pull Request -
State: closed - Opened by jonn-smith about 2 years ago
#140 - How to select models for anno
Issue -
State: open - Opened by hmyh1202 about 2 years ago
- 2 comments
#139 - Updated bulk model name to reflect internal multiplexing.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#138 - Fixed the mas10 model segment names.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#137 - Updated default models to have more intuitive names
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#136 - Updated cd.yml github action for permissions issue
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#135 - Updated github action bumpversion to v0.0.7
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#134 - Added VIM to docker image
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#133 - Fixed bug in header parsing.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
- 1 comment
#132 - Longbow `stats` should include the number of array reads that pass longbow filtering
Issue -
State: open - Opened by jonn-smith over 2 years ago
#131 - Specifying UMI length
Issue -
State: closed - Opened by MVesuviusC over 2 years ago
- 5 comments
#130 - `Segment` annotates all leading array elements with `START` instead of their leading adapter
Issue -
State: open - Opened by jonn-smith over 2 years ago
Labels: bug, High Priority
#129 - Multiple concurrent runs overwriting ._longbow_filter_*.bam?
Issue -
State: closed - Opened by MVesuviusC over 2 years ago
- 7 comments
#128 - Fixed barcode ambiguity bug.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#127 - missing umi and/or cell tag from alligned reads after longbow processing
Issue -
State: open - Opened by khandaud15 over 2 years ago
- 1 comment
#126 - Hotfix for some `correct` stats and parsing model info from bam headers
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#125 - Updates to `pad` and `correct`
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#124 - Correct now automatically allows for barcode padding
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#123 - Added in count of number of reads that could not be corrected.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#122 - Updating `correct` to use symspellpy and a frequency whitelist.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#121 - Aligned data causes longbow tools to crash
Issue -
State: open - Opened by jonn-smith over 2 years ago
Labels: bug, High Priority
#120 - Kvg improve correction behavior
Pull Request -
State: closed - Opened by kvg over 2 years ago
#119 - Investigate test failure for demultiplex command
Issue -
State: closed - Opened by kvg over 2 years ago
- 2 comments
#118 - Fix integration tests to be more independent of each other
Issue -
State: closed - Opened by kvg over 2 years ago
#117 - processes issue
Issue -
State: open - Opened by xc611 over 2 years ago
- 7 comments
#116 - Test framework expansion
Pull Request -
State: closed - Opened by kvg over 2 years ago
#115 - Fix read name hashing.
Pull Request -
State: closed - Opened by kvg over 2 years ago
- 2 comments
#114 - Minor cleanup.
Pull Request -
State: closed - Opened by kvg over 2 years ago
#113 - Generalization to demultiplexing.
Pull Request -
State: closed - Opened by kvg over 2 years ago
#112 - Fixing issue with user-defined models.
Pull Request -
State: closed - Opened by jonn-smith over 2 years ago
#91 - Add automatic bam / pbi indexing when creating files
Issue -
State: open - Opened by jonn-smith over 2 years ago
Labels: enhancement, High Priority
#89 - Review docker build steps to remove experimental docker features.
Issue -
State: closed - Opened by jonn-smith almost 3 years ago
- 1 comment
#87 - Models need more descriptive adapter names.
Issue -
State: closed - Opened by jonn-smith almost 3 years ago
- 1 comment