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

#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

#163 - fixed various bugs and tests

Pull Request - State: closed - Opened by jamestwebber 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

#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

#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

#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

#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