fulcrumgenomics/fgpyo issues and pull requests

#88 - Add MetricWriter to permit streamed writing of metrics

Issue - State: open - Opened by msto 8 months ago
Labels: enhancement

#87 - Reconcile the CI helper script with GitHub Actions

Issue - State: closed - Opened by clintval 8 months ago - 1 comment
Labels: good first issue

#86 - chore: isort

Pull Request - State: closed - Opened by msto 8 months ago - 2 comments

#85 - feat: add SupplementaryAlignment constructor from read

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

#84 - Add a method to calculate MD and NM tags.

Issue - State: open - Opened by nh13 9 months ago
Labels: enhancement, good first issue

#83 - Add a method on Template to fixmate information

Issue - State: open - Opened by nh13 9 months ago
Labels: enhancement

#82 - add a test to explicitly support columns out of order in Metric

Pull Request - State: closed - Opened by nh13 10 months ago - 1 comment

#81 - Add a py.typed file for package to be PEP561 compliant

Pull Request - State: closed - Opened by clintval 10 months ago - 1 comment

#80 - Feature/metric with dataclass or attr

Pull Request - State: closed - Opened by TedBrookings 10 months ago - 4 comments

#79 - Generate code for `SamBuilder` based on an input SAM/BAM

Issue - State: open - Opened by nh13 10 months ago
Labels: enhancement

#78 - Add VCF module to docs and fixup docs warnings

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

#77 - Add a context manager for zipping FASTX files

Pull Request - State: closed - Opened by clintval 10 months ago - 6 comments

#76 - Have ContigBuilder.add() default to adding 1x the bases provided

Pull Request - State: closed - Opened by clintval 10 months ago - 1 comment

#75 - Fix type problems found by latest mypy

Pull Request - State: closed - Opened by TedBrookings 11 months ago - 1 comment

#74 - Feature/support updated mypy nh13

Pull Request - State: closed - Opened by nh13 11 months ago

#73 - Newer versions of mypy reject multiple lines of fgpyo

Issue - State: closed - Opened by TedBrookings 11 months ago

#72 - Recent VCF work is not available in the public docs

Issue - State: closed - Opened by clintval 11 months ago - 1 comment
Labels: documentation

#71 - Fix install and test

Pull Request - State: closed - Opened by TedBrookings 11 months ago - 1 comment

#70 - Metric.read and Metric.write should be context managers

Issue - State: open - Opened by msto 11 months ago - 1 comment

#69 - feat: Support stdin/stdout special cases in sam.reader/writer

Pull Request - State: closed - Opened by msto 11 months ago - 5 comments

#68 - Make ProgressLogger a context manager

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

#67 - Support stdin/stdout in sam.reader and sam.writer

Issue - State: closed - Opened by msto 12 months ago - 1 comment

#65 - refactor: use pathlib in tests

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

#64 - ci: require that the poetry lock file is up to date

Pull Request - State: closed - Opened by nh13 12 months ago - 2 comments

#63 - doc: Use rtd theme

Pull Request - State: closed - Opened by msto 12 months ago - 3 comments

#62 - feat: add Template.write_to()

Pull Request - State: closed - Opened by msto 12 months ago - 1 comment

#61 - feat: add chrom1/chrom2 arguments to add_pair

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

#60 - Add function to write templates directly to file

Issue - State: closed - Opened by msto 12 months ago - 2 comments

#59 - feat: add set_tag method to Template

Pull Request - State: closed - Opened by msto 12 months ago - 1 comment

#58 - feat: add header property

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

#57 - Add PairedFastqReader

Issue - State: closed - Opened by msto about 1 year ago - 6 comments

#56 - Add function to combine headers from multiple AlignmentFiles

Issue - State: open - Opened by msto about 1 year ago - 2 comments

#55 - SamBuilder should permit addition of discordant pairs

Issue - State: closed - Opened by msto about 1 year ago - 1 comment

#54 - Add method is_clipping to CigarOp

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

#53 - fast_concat() for Metric

Pull Request - State: closed - Opened by kockan about 1 year ago - 3 comments

#52 - feat: offer GZIP support for Metric IO

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

#51 - Metric read/write methods should use io.to_reader() and io.to_writer()

Issue - State: closed - Opened by tfenne about 1 year ago
Labels: good first issue

#50 - Metric.read should support skipping extra columns

Pull Request - State: closed - Opened by nh13 about 1 year ago - 1 comment

#49 - Metric classes should allow for _additional_ columns to be present when reading

Issue - State: closed - Opened by nh13 about 1 year ago - 3 comments
Labels: good first issue, help wanted

#48 - Suppress stderr printing when sam indices are older than sam file

Pull Request - State: closed - Opened by TedBrookings about 1 year ago - 2 comments

#47 - Add vcf module

Pull Request - State: closed - Opened by TedBrookings about 1 year ago - 2 comments

#46 - Add a Metric.fast_concat() function to aggregate metrics across files

Issue - State: closed - Opened by tfenne about 1 year ago - 1 comment
Labels: enhancement, good first issue

#45 - Make Metric support attrs & dataclasses

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

#44 - Fixes to sam API docs

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#43 - Add method is_clipping to CigarOp

Issue - State: closed - Opened by nh13 over 1 year ago - 1 comment
Labels: enhancement, good first issue

#42 - Create an equivalent to scala's `Either` class

Issue - State: open - Opened by tfenne over 1 year ago - 3 comments

#41 - Added `Alignment` class

Pull Request - State: open - Opened by jacarey over 1 year ago
Labels: good first issue, help wanted

#40 - Added `Alignment` class

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

#39 - Update the docs for new modules

Pull Request - State: closed - Opened by nh13 over 1 year ago - 2 comments

#38 - Fix black formatting in #37

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#37 - add support for unmapped BAM file reading

Pull Request - State: closed - Opened by danielmarrama over 1 year ago - 2 comments

#36 - Comments should go after constants

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

#35 - Update .readthedocs.yml

Pull Request - State: closed - Opened by nh13 over 1 year ago - 3 comments

#34 - [feat] adding column_it to fgpyo.util.string

Pull Request - State: closed - Opened by nh13 over 1 year ago - 1 comment

#33 - Proposed solution for Issue #31

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 1 comment

#32 - sam.reader should support reading unmapped BAMs

Issue - State: closed - Opened by nh13 over 1 year ago - 1 comment
Labels: good first issue

#31 - ProgressLogger should have a `record(rec: AlignedSegment)` function

Issue - State: closed - Opened by tfenne over 1 year ago - 7 comments

#30 - Proposed solution for issue #11

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 1 comment

#29 - Proposed solution for Issue #9

Pull Request - State: closed - Opened by sam-white04 over 1 year ago

#28 - Remove square brackets when writing lists to disk

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 1 comment

#27 - Created unit tests designed to fail pertaining to issue #9

Pull Request - State: closed - Opened by sam-white04 over 1 year ago - 1 comment

#26 - Feature/ samtools typehinted wrappers

Pull Request - State: open - Opened by NatPRoach almost 2 years ago - 1 comment
Labels: help wanted

#25 - Adding the option to specify the sort order of an output SAM file produced by SamBuilder.

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

#24 - Reference set builder dev

Pull Request - State: closed - Opened by sam-white04 almost 2 years ago - 1 comment

#23 - Let the pysam requirement float.

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