mamarjan/gff3-pltools

Issues

• More refactoring wanted!

  #75 opened 12 years ago by lomereiter
  1

• gff3-filter throws exception when field can't be converted to int or float

  #74 opened 12 years ago by mamarjan
  2

• empty operand in filtering expression

  #73 opened 12 years ago by mamarjan
  0

• AttributeValue constructors

  #65 opened 12 years ago by lomereiter
  1

• Improve README and docs

  #62 opened 12 years ago by mamarjan
  1

• refactor Record.append_to

  #66 opened 12 years ago by lomereiter
  5

• Include the tools in Galaxy

  #69 opened 12 years ago by mamarjan
  1

• Make rake build the tools by default

  #70 opened 12 years ago by pjotrp
  2

• Numerical comparison for filtering

  #53 opened 12 years ago by mamarjan
  1

• Length of transcripts for filtering

  #54 opened 12 years ago by mamarjan
  1

• Add support for "and" and "or" in filtering on the command line

  #58 opened 12 years ago by mamarjan
  1

• MAN pages for utilities

  #43 opened 12 years ago by mamarjan
  1

• gff3-ffetch segfaults

  #71 opened 12 years ago by pjotrp
  2

• A tool for correctly grouping all records into features

  #60 opened 12 years ago by mamarjan
  0

• Tool for grouping features and output them in JSON format

  #56 opened 12 years ago by mamarjan
  0

• JSON output

  #55 opened 12 years ago by mamarjan
  2

• GFF3 to JSON tool

  #51 opened 12 years ago by mamarjan
  1

• Output only selected fields in a table format

  #63 opened 12 years ago by mamarjan
  2

• Support for adding a header before the data when selecting columns

  #68 opened 12 years ago by mamarjan
  0

• Output in CSV instead of tab delimited columns

  #67 opened 12 years ago by mamarjan
  0

• GFF3 to GTF and vice versa

  #64 opened 12 years ago by mamarjan
  1

• GTF support

  #52 opened 12 years ago by mamarjan
  2

• Improve validation speed

  #59 opened 12 years ago by mamarjan
  2

• A tool for sorting GFF3 files

  #61 opened 12 years ago by mamarjan
  0

• Filtering features

  #57 opened 12 years ago by mamarjan
  0

• Records to represent pragmas and comments

  #50 opened 12 years ago by mamarjan
  1

• GDC support

  #44 opened 12 years ago by mamarjan
  1

• Ruby interface for validation of GFF3 files

  #39 opened 12 years ago by mamarjan
  1

• A new repository for the Ruby gem

  #49 opened 12 years ago by mamarjan
  1

• Add toString and recursiveToString for Feature

  #48 opened 12 years ago by mamarjan
  0

• A gem for rubygems.org

  #42 opened 12 years ago by mamarjan
  2

• gff3-ffetch to pass FASTA data to output

  #46 opened 12 years ago by mamarjan
  1

• count-features utility too slow

  #33 opened 12 years ago by mamarjan
  1

• A tool for sorting GFF3 files

  #47 opened 12 years ago by mamarjan
  0

• Windows binaries

  #45 opened 12 years ago by mamarjan
  0

• Packaging for Ubuntu 32 and 64 bit

  #36 opened 12 years ago by mamarjan
  4

• Docs

  #40 opened 12 years ago by mamarjan
  1

• New name

  #35 opened 12 years ago by mamarjan
  1

• Ruby interface for filtering GFF3 files

  #38 opened 12 years ago by mamarjan
  0

• & and , have special meaning in attributes field

  #37 opened 12 years ago by mamarjan
  2

• Try re-implementing the FeatureCache using built-in associative arrays

  #41 opened 12 years ago by mamarjan
  0

• Basic GFF3 output in D

  #34 opened 12 years ago by mamarjan
  2

• Move fasta stuff in gff3.d

  #24 opened 12 years ago by pjotrp
  1

• replace_url_escaped_chars() too slow

  #30 opened 12 years ago by mamarjan
  11

• Benchmark tool seg-fault

  #31 opened 12 years ago by mamarjan
  12

• Too many files starting with gff3

  #32 opened 12 years ago by mamarjan
  0

• A utility for benchmarking the parser

  #29 opened 12 years ago by mamarjan
  0

• Refactor RecordRange

  #25 opened 12 years ago by pjotrp
  1

• Validation of record formatting should be lazy

  #26 opened 12 years ago by pjotrp
  0

• Move validation out into its own module

  #27 opened 12 years ago by pjotrp
  1