csw bioruby-maf issues - Githubissues

csw / bioruby-maf

MAF parser for BioRuby

MIT License

11 stars 6 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

problem with bedfile and index file

#122 xzhuo opened 8 years ago
0
For issue #55

#121 dScarpino opened 8 years ago
0
Rewind parser after reaching EOF #55

#120 dScarpino opened 8 years ago
0
Rewind parser after reaching EOF #55

#119 dScarpino opened 8 years ago
2
Rewind parser after reaching EOF #55

#118 dScarpino opened 8 years ago
0
Bio-maf not working with new MAF-files

#117 ghost opened 9 years ago
1
A fatal error has been detected by the Java Runtime Environment

#116 lumiratos closed 10 years ago
2
Some specific details about the maf_bgzip tool

#115 lumiratos opened 10 years ago
8
Problem executing binaries: `extractor_fmt': undefined method `sort_by!'

#114 lumiratos closed 10 years ago
3
Add result concatenation to Tiler and/or maf_tile

#113 csw closed 2 years ago
0
Handle empty MAF files

#112 csw closed 12 years ago
0
Error out in maf_bgzip if output files exist

#111 csw closed 12 years ago
0
Apply Access block filter in #slice

#110 csw closed 12 years ago
0
Only open indexes as needed in Access

#109 csw closed 12 years ago
0
Work on Kyoto Cabinet performance with large files

#108 csw closed 12 years ago
1
Add option for 1-based intervals

#107 csw closed 12 years ago
0
Add extended UCSC bin support

#106 csw closed 12 years ago
0
Bail on newer index formats

#105 csw closed 12 years ago
0
Measure mode performance

#104 csw closed 12 years ago
2
Be more conservative with memory while indexing

#103 csw closed 12 years ago
1
Decide how to handle inconsistent reference sequences

#102 csw closed 2 years ago
0
Eliminate all use of bare "rescue"

#101 csw closed 12 years ago
0
Validate parsing against all UCSC MAF files

#100 csw closed 2 years ago
2
Develop Galaxy wrappers

#99 csw closed 2 years ago
0
Track BGZF block spilling

#98 csw closed 12 years ago
1
Index secondary sequences

#97 csw closed 12 years ago
0
Allow specifying tiling fill character

#96 csw closed 12 years ago
0
Return block RV from Access#tile

#95 csw closed 12 years ago
1
Return tiled alignments in a more usable form

#94 csw closed 12 years ago
0
Look for use cases with other MAF tools

#93 csw closed 2 years ago
0
Add CLI tools for indexed extraction, slicing

#92 csw closed 12 years ago
0
#slice output is incorrect

#91 csw closed 12 years ago
0
Investigate using different characters for gaps

#90 csw closed 2 years ago
0
Accept sequence with --interval arg to maf_tile

#89 csw closed 12 years ago
0
Tiling: get species list from index data if needed

#88 csw closed 2 years ago
0
Do not return blocks with no sequences

#87 csw closed 12 years ago
2
Refactor MAFParsing#postprocess_block as filter

#86 csw closed 12 years ago
0
On-the-fly MAF indexing

#85 csw closed 12 years ago
1
Check reverse complement handling

#84 csw closed 2 years ago
1
Straighten out nomenclature for MAF operations

#83 csw closed 12 years ago
1
Support directory-based access with CLI tools

#82 csw closed 12 years ago
1
Add Cucumber/Aruba features for CLI tools

#81 csw closed 12 years ago
0
Add Nailgun support

#80 csw closed 2 years ago
1
Chop blocks when searching in a given interval

#79 csw closed 12 years ago
1
Join blocks after filtering species

#78 csw closed 12 years ago
1
Make index scan threads configurable

#77 csw closed 2 years ago
0
Discrepancy in index scan results vs. bx-python

#76 csw closed 12 years ago
1
Compare index search performance against bx-python

#75 csw closed 2 years ago
1
Explore generalizing the indexing code

#74 csw closed 2 years ago
0
Stitch adjacent blocks together

#73 csw closed 12 years ago
1