csw/bioruby-maf issues and pull requests

#122 - problem with bedfile and index file

Issue - State: open - Opened by xzhuo over 8 years ago

#121 - For issue #55

Pull Request - State: open - Opened by dScarpino over 8 years ago

#120 - Rewind parser after reaching EOF #55

Pull Request - State: open - Opened by dScarpino over 8 years ago

#119 - Rewind parser after reaching EOF #55

Pull Request - State: open - Opened by dScarpino over 8 years ago - 2 comments

#118 - Rewind parser after reaching EOF #55

Pull Request - State: open - Opened by dScarpino over 8 years ago

#117 - Bio-maf not working with new MAF-files

Issue - State: open - Opened by ghost almost 10 years ago - 1 comment

#116 - A fatal error has been detected by the Java Runtime Environment

Issue - State: closed - Opened by lumiratos over 10 years ago - 2 comments

#115 - Some specific details about the maf_bgzip tool

Issue - State: open - Opened by lumiratos over 10 years ago - 8 comments

#114 - Problem executing binaries: `extractor_fmt': undefined method `sort_by!'

Issue - State: closed - Opened by lumiratos over 10 years ago - 3 comments

#113 - Add result concatenation to Tiler and/or maf_tile

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, medium

#112 - Handle empty MAF files

Issue - State: closed - Opened by csw about 12 years ago
Labels: bug, medium

#111 - Error out in maf_bgzip if output files exist

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#110 - Apply Access block filter in #slice

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#109 - Only open indexes as needed in Access

Issue - State: closed - Opened by csw about 12 years ago
Labels: bug, easy

#108 - Work on Kyoto Cabinet performance with large files

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: bug, medium

#107 - Add option for 1-based intervals

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#106 - Add extended UCSC bin support

Issue - State: closed - Opened by csw about 12 years ago
Labels: bug, medium

#105 - Bail on newer index formats

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#104 - Measure mode performance

Issue - State: closed - Opened by csw about 12 years ago - 2 comments
Labels: enhancement, medium

#103 - Be more conservative with memory while indexing

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: bug, easy

#102 - Decide how to handle inconsistent reference sequences

Issue - State: closed - Opened by csw about 12 years ago
Labels: bug, question, medium

#101 - Eliminate all use of bare "rescue"

Issue - State: closed - Opened by csw about 12 years ago
Labels: bug, easy

#100 - Validate parsing against all UCSC MAF files

Issue - State: closed - Opened by csw about 12 years ago - 2 comments
Labels: medium

#99 - Develop Galaxy wrappers

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, hard

#98 - Track BGZF block spilling

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, medium

#97 - Index secondary sequences

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, medium

#96 - Allow specifying tiling fill character

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#95 - Return block RV from Access#tile

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, easy

#94 - Return tiled alignments in a more usable form

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, medium

#93 - Look for use cases with other MAF tools

Issue - State: closed - Opened by csw about 12 years ago
Labels: question, specs

#92 - Add CLI tools for indexed extraction, slicing

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, medium

#91 - #slice output is incorrect

Issue - State: closed - Opened by csw about 12 years ago
Labels: bug, medium

#90 - Investigate using different characters for gaps

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, question, medium

#89 - Accept sequence with --interval arg to maf_tile

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#88 - Tiling: get species list from index data if needed

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, medium

#87 - Do not return blocks with no sequences

Issue - State: closed - Opened by csw about 12 years ago - 2 comments
Labels: bug, medium

#86 - Refactor MAFParsing#postprocess_block as filter

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#85 - On-the-fly MAF indexing

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, easy

#84 - Check reverse complement handling

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: bug, medium

#83 - Straighten out nomenclature for MAF operations

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: bug, medium

#82 - Support directory-based access with CLI tools

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, easy

#81 - Add Cucumber/Aruba features for CLI tools

Issue - State: closed - Opened by csw about 12 years ago
Labels: medium, specs

#80 - Add Nailgun support

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, jruby

#79 - Chop blocks when searching in a given interval

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, medium

#78 - Join blocks after filtering species

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, medium

#77 - Make index scan threads configurable

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#76 - Discrepancy in index scan results vs. bx-python

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: bug, medium

#75 - Compare index search performance against bx-python

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: question

#74 - Explore generalizing the indexing code

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, hard

#73 - Stitch adjacent blocks together

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, medium

#72 - Compile list of extant MAF filter/query features

Issue - State: closed - Opened by csw about 12 years ago
Labels: specs

#71 - Evaluate search-by-feature with GTF files etc

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement

#70 - Convert blocks and sequences to bio-alignment representation

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, medium

#69 - Investigate compression formats to support

Issue - State: closed - Opened by csw about 12 years ago
Labels: question

#68 - Expose 'i' data in a more usable way

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, easy

#67 - Parallelize sequential parsing

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, hard

#66 - Revisit Enumerator usage

Issue - State: closed - Opened by csw about 12 years ago
Labels: enhancement, easy

#65 - Add multiple index support

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, medium

#64 - Add BGZF support

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, hard

#63 - Fix gemspec, gem building

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: bug, medium

#62 - Add ways of reading reference sequence efficiently

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, easy

#61 - Add postprocessing options

Issue - State: closed - Opened by csw about 12 years ago - 1 comment
Labels: enhancement, easy

#60 - Add CLI tiling tool

Issue - State: closed - Opened by csw about 12 years ago - 2 comments
Labels: enhancement, easy

#59 - Ensure blocks can be returned in sorted order

Issue - State: closed - Opened by csw over 12 years ago - 3 comments
Labels: bug, medium

#58 - Tiling alignment block data with reference sequence

Pull Request - State: closed - Opened by csw over 12 years ago - 1 comment

#57 - Evaluate what to do with 'i' lines when filtering data

Issue - State: closed - Opened by csw over 12 years ago
Labels: question

#56 - race condition in Parser#parse_blocks_parallel

Issue - State: closed - Opened by csw over 12 years ago
Labels: bug, easy

#55 - Rewind parser after reaching EOF

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, easy

#54 - Refactor worker thread management

Issue - State: closed - Opened by csw over 12 years ago
Labels: medium

#53 - Use reference sequence for joining MAF blocks

Issue - State: closed - Opened by csw over 12 years ago - 2 comments
Labels: enhancement, medium

#52 - Remove gaps after filtering species

Pull Request - State: closed - Opened by csw over 12 years ago - 1 comment

#51 - Memoize seq_filter_ok?

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, easy

#50 - Investigate creating platform-specific gems

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, medium

#49 - Break out Kyoto Cabinet Java support into its own gem

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, hard, jruby

#48 - attr_accessors

Issue - State: open - Opened by pjotrp over 12 years ago - 1 comment

#47 - Exceptions on parsing

Issue - State: open - Opened by pjotrp over 12 years ago - 1 comment

#46 - Using the splat operator

Issue - State: closed - Opened by pjotrp over 12 years ago

#45 - Removed rvmrc and started on Debian build instructions

Pull Request - State: closed - Opened by pjotrp over 12 years ago - 6 comments

#44 - remove .rvmrc file from git repo

Issue - State: closed - Opened by pjotrp over 12 years ago - 2 comments

#43 - MAF output

Issue - State: closed - Opened by csw over 12 years ago - 2 comments
Labels: enhancement, medium

#42 - Small Cosmetic Cleanups

Pull Request - State: closed - Opened by GeekOnCoffee over 12 years ago - 1 comment

#41 - Parallelize parsing

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, hard, jruby

#40 - Need to return results from KyotoIndex#find with an Enumerator

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, medium

#39 - Handle i, e, q lines

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, easy

#38 - Detect overlaps at index build time

Issue - State: closed - Opened by csw over 12 years ago - 2 comments
Labels: enhancement, easy

#37 - Optimize block overlap tests on index scans

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, easy

#34 - Create random BED file generator

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, easy

#33 - Need to load @species in KyotoIndex

Issue - State: closed - Opened by csw over 12 years ago
Labels: bug, easy

#32 - Generate binary format layout illustrations with struct library

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, medium

#31 - Sequence filters break when running full RSpec suite under JRuby

Issue - State: closed - Opened by csw over 12 years ago - 5 comments
Labels: bug

#30 - Eliminate gaps after removing species

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, question, medium

#23 - Record index format version

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, easy

#22 - Filter alignment blocks

Issue - State: closed - Opened by csw over 12 years ago - 2 comments
Labels: enhancement

#20 - Experiment with Ragel parser

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, medium

#19 - Sort index data before loading into Kyoto Cabinet

Issue - State: closed - Opened by csw over 12 years ago - 1 comment
Labels: enhancement, medium

#17 - Add JRuby compatibility for Kyoto Cabinet

Issue - State: closed - Opened by csw over 12 years ago - 3 comments
Labels: enhancement, medium, jruby

#12 - Consider pulling out UCSC bin code as a separate gem

Issue - State: closed - Opened by csw over 12 years ago - 3 comments
Labels: enhancement

#7 - Need proper README

Issue - State: closed - Opened by csw over 12 years ago - 3 comments
Labels: enhancement, easy

#5 - Handle chunks with no block starts

Issue - State: closed - Opened by csw over 12 years ago
Labels: bug

#3 - Lazily parse variables

Issue - State: closed - Opened by csw over 12 years ago
Labels: enhancement, easy

GitHub / csw/bioruby-maf issues and pull requests