PeteHaitch/methtuple issues and pull requests

#104 - Error message

Issue - State: closed - Opened by weishwu over 2 years ago - 11 comments

#103 - Fix issue #102

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

#102 - nonCG, single context reporting

Issue - State: closed - Opened by amvondras almost 3 years ago - 5 comments

#101 - Parsing SAM rather than BAM

Issue - State: closed - Opened by PeteHaitch over 8 years ago
Labels: enhancement

#100 - Broken with pysam v0.8.4

Issue - State: closed - Opened by PeteHaitch almost 9 years ago - 7 comments
Labels: bug

#99 - Relevant changes in Bismark v0.14.4

Issue - State: open - Opened by PeteHaitch about 9 years ago - 1 comment
Labels: question, ready

#98 - Tests failing under pysam v0.8.3

Issue - State: closed - Opened by PeteHaitch about 9 years ago
Labels: bug

#97 - Improve check that paired-end BAM is sorted by queryname

Issue - State: closed - Opened by PeteHaitch over 9 years ago - 4 comments
Labels: enhancement, for-paper

#96 - Support coveralls.io

Issue - State: closed - Opened by PeteHaitch over 9 years ago
Labels: enhancement

#95 - Upgrade to pysam v0.8.2

Issue - State: closed - Opened by PeteHaitch over 9 years ago
Labels: enhancement

#94 - Update to pysam 0.8.1

Issue - State: closed - Opened by PeteHaitch over 9 years ago - 2 comments

#93 - Using iterators

Issue - State: closed - Opened by PeteHaitch about 10 years ago - 1 comment
Labels: enhancement, low-priority

#92 - Add ac to filename of tsp files created with —all-combinations.

Pull Request - State: closed - Opened by PeteHaitch about 10 years ago

#91 - All pairs

Pull Request - State: closed - Opened by PeteHaitch about 10 years ago

#90 - Processing soft-clipped reads

Issue - State: open - Opened by PeteHaitch about 10 years ago - 1 comment
Labels: enhancement

#89 - Indel support

Pull Request - State: closed - Opened by PeteHaitch about 10 years ago

#88 - Better handling of multiple methylation types

Issue - State: closed - Opened by PeteHaitch about 10 years ago - 1 comment
Labels: bug, for-paper

#87 - Supporting other aligners

Issue - State: closed - Opened by PeteHaitch about 10 years ago - 3 comments
Labels: enhancement, low-priority

#86 - Option to create maximal m-tuple per read

Issue - State: closed - Opened by PeteHaitch about 10 years ago - 1 comment
Labels: enhancement

#85 - Option to create all possible m-tuples

Issue - State: closed - Opened by PeteHaitch about 10 years ago - 1 comment
Labels: enhancement

#84 - Note regarding --of Bismark

Issue - State: closed - Opened by PeteHaitch about 10 years ago
Labels: enhancement

#83 - Check default EOL character in .tsv files.

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: question

#82 - Improve README

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#81 - Add strand

Pull Request - State: closed - Opened by PeteHaitch over 10 years ago

#80 - Include strand in output?

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: question

#79 - Set default ir1p or ir2p

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 2 comments
Labels: bug

#78 - More options for run_comethylation.sh

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment

#77 - Ignore by seq cycle

Pull Request - State: closed - Opened by PeteHaitch over 10 years ago

#76 - Add native parallel support to comethylation

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#75 - Python3 support

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 8 comments
Labels: enhancement

#74 - Simplify command line arguments

Issue - State: closed - Opened by PeteHaitch over 10 years ago
Labels: enhancement

#73 - Supporting aligners besides Bismark

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#72 - Is CHG methylation strand-symmetric?

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: question

#71 - More general filtering by cycle

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#70 - Benchmarking

Issue - State: open - Opened by PeteHaitch over 10 years ago - 4 comments
Labels: enhancement, for-paper

#69 - Add option to gzip output

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#68 - Use GNU parallel in helper script

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#67 - Add to PyPI

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 2 comments
Labels: enhancement

#66 - Acknowledgements

Issue - State: closed - Opened by PeteHaitch over 10 years ago

#65 - Update examples using newest version of bismark

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 4 comments

#64 - Improve memory usage

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 5 comments

#63 - python setup.py test has exit status 1

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 2 comments
Labels: bug

#62 - Handle PBAT libraries

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: enhancement

#61 - Handle non-directional protocols

Issue - State: closed - Opened by PeteHaitch over 10 years ago
Labels: enhancement

#60 - Make a strand/orientation checking function

Issue - State: closed - Opened by PeteHaitch over 10 years ago
Labels: enhancement

#59 - Remove unused files for initial public release

Issue - State: closed - Opened by PeteHaitch over 10 years ago

#58 - Changing name from Comethylation to comethylation

Issue - State: closed - Opened by PeteHaitch over 10 years ago - 1 comment
Labels: bug

#57 - Test whether read contains complicated cigar and skip read if it does

Issue - State: closed - Opened by PeteHaitch over 10 years ago
Labels: enhancement

#56 - Add Travis CI integration

Issue - State: closed - Opened by PeteHaitch over 10 years ago
Labels: enhancement

#55 - Reinstated tests folder on add_tests branch

Pull Request - State: closed - Opened by PeteHaitch over 10 years ago

#54 - Allow multiple methylation types

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: enhancement

#53 - Test against non-directional data

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: bug

#52 - Simplify command line arguments

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: bug

#51 - Ensure scripts fail gracefully if packages aren't available

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: bug

#50 - Write `QNAME` of reads that failed QC to a separate file

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 2 comments
Labels: enhancement

#49 - Helpful error messages

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: enhancement

#48 - Decide on names of concepts

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: bug

#47 - Change all references to n-tuple to m-tuple

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: bug

#46 - Include helper scripts

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: enhancement

#45 - `comethylation` may not work with soft-clipped reads or reads containing indels

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 10 comments
Labels: bug

#44 - Include `README`

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: duplicate

#43 - `chromosome_index` is hard-coded

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: bug

#42 - Write Histogram of number of CG/CHG/CHH methylation loci per DNA fragment to file

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: duplicate

#41 - Deprecate `--pairChoice` option

Issue - State: closed - Opened by PeteHaitch almost 11 years ago

#38 - Check all scripts for compatibility with latest version of pysam

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 2 comments
Labels: bug

#37 - Write histogram of CpGs per read to a separate file

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: enhancement

#36 - Add option to filter reads by `MAPQ` in `comethylation.py`

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: enhancement

#35 - Include test data in the initial public release

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: duplicate

#34 - Rewrite `correct_Bismark_PE_SAM.py`

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: enhancement

#33 - Make sure `bismarify.py` can deal with a BAM that doesn't already have a `@PG` tag in the header

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: bug

#32 - Allow `bismarkify.py` to write to STDOUT

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: enhancement

#31 - Allow methtuple to process a BAM from STDIN

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: enhancement, for-paper

#30 - bismarkify.py

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 5 comments
Labels: enhancement

#29 - Add automatic updating of `@PG` tag when updates are made to `bismarkify.py`

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment
Labels: bug

#28 - Make all scripts executable

Issue - State: closed - Opened by PeteHaitch almost 11 years ago

#27 - Improve logging data

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: duplicate

#26 - Add proper version numbers to all scripts

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 1 comment

#25 - Add support for reads containing INDELs

Issue - State: closed - Opened by PeteHaitch almost 11 years ago - 3 comments
Labels: enhancement

#24 - Check that `--oldBismark` flags works correctly

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: enhancement

#23 - Include `--mTuple` and `--methylationType` parameters in output filenames

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: enhancement

#22 - Choose license

Issue - State: closed - Opened by PeteHaitch almost 11 years ago
Labels: enhancement

#20 - Add filtering by MAPQ

Issue - State: closed - Opened by PeteHaitch about 11 years ago - 1 comment
Labels: duplicate

#19 - Notes on SAM/BAM files created by BSmooth

Issue - State: closed - Opened by PeteHaitch about 11 years ago - 2 comments

#18 - Add `--strandCollapse` or `--noStrandCollapse` option

Issue - State: closed - Opened by PeteHaitch about 11 years ago - 1 comment
Labels: enhancement

#17 - Gracefully fail for reads without XM-, XR- or XG-tags

Issue - State: closed - Opened by PeteHaitch about 11 years ago - 1 comment
Labels: bug

#16 - Begin adding support for reads containing INDELs to both bismarkify.py a...

Pull Request - State: closed - Opened by PeteHaitch over 11 years ago - 1 comment

#15 - Refine process for dealing with overlapping read-pairs (part 2)

Issue - State: closed - Opened by PeteHaitch over 11 years ago - 1 comment
Labels: enhancement

#14 - Parse SAM/BAM header to extract useful information

Issue - State: closed - Opened by PeteHaitch over 11 years ago - 1 comment
Labels: enhancement

#13 - Allow ignoring of a different number of bases for read_1 and read_2 in PE data

Issue - State: closed - Opened by PeteHaitch over 11 years ago
Labels: bug

#11 - Add a --bismark option to directly process SAM/BAM files created by Bismark, i.e. allowing for the non-compliant FLAG and read name suffixes imposed by Bismark.

Issue - State: closed - Opened by PeteHaitch over 11 years ago - 2 comments
Labels: enhancement

GitHub / PeteHaitch/methtuple issues and pull requests