Ecosyste.ms: Issues

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GitHub / jbloomlab/alignparse issues and pull requests

#103 - some tweaks to build docs and pass linting

Pull Request - State: closed - Opened by jbloom 3 months ago

#102 - Read accuracy vs. empirical accuracy

Issue - State: closed - Opened by krdav 6 months ago - 2 comments

#100 - Fix tempfile mode error in minimap2.py

Pull Request - State: closed - Opened by jianfcpku 6 months ago - 2 comments

#99 - Probably a bug in minimap2 error handling?

Issue - State: closed - Opened by jianfcpku 6 months ago - 2 comments

#98 - possible bug with indel consensus?

Issue - State: closed - Opened by tylernstarr 12 months ago - 4 comments

#97 - require python 3.8 or higher (becomes version 0.6.2)

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

#96 - f"string=" issue

Issue - State: closed - Opened by Jayaos over 1 year ago - 2 comments

#95 - pass tests with newer dependency versions (becomes 0.6.1)

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

#94 - update reportfile parsing for ccs v6

Pull Request - State: closed - Opened by andrewwbutler about 2 years ago - 5 comments

#93 - Handle tags of type B

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

#92 - minimap2 module: retain ML:B tag

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

#91 - `MutationRenumber` accepts `allow_letter_suffixed_numbers`

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

#90 - remove deprecated pandas append

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

#89 - `pandas` has deprecated `append`

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

#88 - fix error message

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

#87 - `MutationRenumber` accepts gaps / stop (version 0.4)

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

#86 - in-frame indels as subs and more consensus calling options (v 0.3.0)

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

#85 - resent index in `add_mut_info_cols`

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

#84 - use newer versions for mybinder

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

#83 - MyBinder Connection Failed

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

#82 - What do {'spacer', 'termini3', 'gene', 'termini5'} each represent?

Issue - State: closed - Opened by xguse over 3 years ago - 1 comment

#81 - Why use Genbank's type for your feature name?

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

#80 - Merge consecutive deletions

Pull Request - State: closed - Opened by Bernadetadad over 3 years ago - 6 comments

#79 - require `numpy` >= 1.17

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

#78 - fix bug causing in error `simple_mutconsensus` when 1 `group_col`

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

#77 - `consensus` module handles negative sites (v 0.2.3)

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

#76 - Handle negative sites

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

#75 - add `sort_mutations` (version to 0.2.1)

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

#74 - added `utils.MutationRenumber` (version to 0.2.0)

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

#73 - Removed `--for-only` from `OPTIONS_VIRUS_W_DEL`

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

#72 - Strand alignment with OPTIONS_VIRUS_W_DEL

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

#71 - parse n passes tags from `ccs` version 5.0 FASTQs

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

#70 - parse passes from `ccs` version 5.0 FASTQ ccs files

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

#69 - parse summary from `ccs` version 5.0

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

#68 - added `hspace` as parameter to `Targets.plot`

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

#67 - fix spelling of acknowledgements

Pull Request - State: closed - Opened by khdcrawford almost 5 years ago - 2 comments

#66 - Citation/acknowledgements

Issue - State: closed - Opened by afrubin almost 5 years ago - 1 comment

#65 - added `select_target_names` option to `Targets`

Pull Request - State: closed - Opened by jbloom almost 5 years ago - 1 comment

#64 - Citation info

Pull Request - State: closed - Opened by khdcrawford almost 5 years ago

#63 - updated zenodo metadata description

Pull Request - State: closed - Opened by khdcrawford almost 5 years ago

#62 - updated zenodo metadata

Pull Request - State: closed - Opened by khdcrawford almost 5 years ago - 2 comments

#61 - add zenodo badge

Pull Request - State: closed - Opened by khdcrawford almost 5 years ago

#60 - README better explains Python versions

Pull Request - State: closed - Opened by jbloom almost 5 years ago

#59 - Review edits

Pull Request - State: closed - Opened by khdcrawford almost 5 years ago - 4 comments

#58 - PySAM problems with Python 3.8 + OS X

Issue - State: closed - Opened by bede almost 5 years ago - 5 comments

#57 - JOSS review suggestions

Pull Request - State: closed - Opened by afrubin almost 5 years ago

#56 - Lassa virus example/other aligners in manuscript

Issue - State: closed - Opened by afrubin almost 5 years ago - 2 comments

#55 - Support for compressed input files

Issue - State: closed - Opened by afrubin almost 5 years ago - 2 comments

#54 - Version requirement for minimap2?

Issue - State: closed - Opened by afrubin almost 5 years ago - 2 comments

#53 - YAML + FASTA or YAML only input files

Issue - State: closed - Opened by afrubin almost 5 years ago - 2 comments

#52 - Update paper so it compiles

Pull Request - State: closed - Opened by arfon about 5 years ago

#51 - Paperedits - final edits

Pull Request - State: closed - Opened by khdcrawford about 5 years ago

#50 - paper markdown formatting edits

Pull Request - State: closed - Opened by khdcrawford about 5 years ago

#49 - initial submission of JOSS paper describing package

Pull Request - State: closed - Opened by jbloom about 5 years ago

#48 - Docs

Pull Request - State: closed - Opened by khdcrawford about 5 years ago

#47 - dependencies for mybinder

Issue - State: closed - Opened by jbloom about 5 years ago - 1 comment

#46 - JOSS paper

Issue - State: closed - Opened by jbloom about 5 years ago - 2 comments

#45 - expand README

Issue - State: closed - Opened by jbloom about 5 years ago - 2 comments

#44 - add `mybinder` link to examples

Issue - State: closed - Opened by jbloom about 5 years ago - 1 comment

#43 - LASV example targets / parse specs

Issue - State: closed - Opened by jbloom about 5 years ago - 2 comments

#42 - add hyperlinks to API in example notebooks

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

#41 - Multiple targets example

Pull Request - State: closed - Opened by khdcrawford about 5 years ago

#40 - Filter supplementary alignments

Pull Request - State: closed - Opened by khdcrawford about 5 years ago - 7 comments

#39 - Set up to automatically run travis CI tests

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#38 - Added option to return `cs` of feature that fails filter.

Pull Request - State: closed - Opened by khdcrawford about 5 years ago - 5 comments

#37 - Specify `.csv` name in `parse_alignment`

Issue - State: closed - Opened by khdcrawford about 5 years ago - 2 comments

#36 - Add more info about filtered reads

Issue - State: closed - Opened by khdcrawford about 5 years ago - 2 comments

#35 - add examples to docs

Pull Request - State: closed - Opened by jbloom about 5 years ago

#34 - added functionality for parsing virus with deletions

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#33 - RecA DMS example expanded to illustrate `consensus` module

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#32 - `ccs.Summary` handles reports from PacBio `ccs` 4

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#31 - `OSError: [Errno 12] Cannot allocate memory` with `ccs.Summaries()`

Issue - State: closed - Opened by khdcrawford about 5 years ago - 2 comments

#30 - `ccs.Summaries` works without report, `np` tag

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#29 - add ability to get "accuracy" of features

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#28 - add `Targets.align_and_parse`

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#27 - profiling and optimization

Pull Request - State: closed - Opened by jbloom about 5 years ago - 2 comments

#26 - small tweaks to `minimap2` module

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#25 - updated `VEP_pilot` notebook to run `parse_alignment`

Pull Request - State: closed - Opened by khdcrawford about 5 years ago

#24 - Test on real-size data

Issue - State: closed - Opened by jbloom about 5 years ago - 3 comments

#23 - Flesh out `VEP` example -- or just make private tests?

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

#22 - Expand example to show use of `consensus` module.

Issue - State: closed - Opened by jbloom about 5 years ago - 1 comment

#21 - test `Targets.parse_alignment`.

Issue - State: closed - Opened by jbloom about 5 years ago - 1 comment

#20 - Implements `Targets.parse_alignment`

Pull Request - State: closed - Opened by jbloom about 5 years ago - 1 comment

#18 - Allow single `feature_parse_specs` dict for multiple targets

Issue - State: closed - Opened by khdcrawford over 5 years ago - 2 comments

#17 - flesh out docs and structure for `Targets.parse_alignment`.

Issue - State: closed - Opened by jbloom over 5 years ago - 2 comments

#16 - Add to `cs_parse` module functions to parse `cs` strings

Issue - State: closed - Opened by jbloom over 5 years ago - 1 comment

#15 - Refactor VEP example notebook to work with `Targets` having `feature_parse_specs`.

Issue - State: closed - Opened by jbloom over 5 years ago - 1 comment

#13 - implements `Targets.parse_alignment_cs`

Pull Request - State: closed - Opened by jbloom over 5 years ago - 1 comment

#12 - Add cs_parse

Pull Request - State: closed - Opened by khdcrawford over 5 years ago

#11 - add `consensus` module

Pull Request - State: closed - Opened by jbloom over 5 years ago - 1 comment

#10 - fix typo in `Target.__repr__`

Pull Request - State: closed - Opened by jbloom over 5 years ago - 1 comment

#9 - `ccs.Summaries` handles reports from `ccs` 3.4.1

Pull Request - State: closed - Opened by jbloom over 5 years ago - 1 comment

#8 - `retain_tags` option for `minimap2.Mapper`.

Pull Request - State: closed - Opened by jbloom over 5 years ago - 1 comment

#7 - implement `minimap2` alignment

Pull Request - State: closed - Opened by jbloom over 5 years ago - 2 comments

#6 - deleted unneeded files

Pull Request - State: closed - Opened by jbloom over 5 years ago

#5 - add `align` and `parse_alignment` to `Targets`

Pull Request - State: closed - Opened by jbloom over 5 years ago

#4 - add VEP to examples

Pull Request - State: closed - Opened by jbloom over 5 years ago