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Changeset [eebacea01205971c19a374cbcf2cc1c00744d195] by Robert Buels

Revision eebacea01205971c19a374cbcf2cc1c00744d195, committed by Robert Buels · January 3rd, 2013 @ 11:04 AM

change names.json files to names.txt files, which are a hybrid line-based/JSON format: one JSON array per line. this makes it easy to incrementally parse the names.txt files, which greatly reduces the memory footprint of generate-names.pl.
https://github.com/GMOD/jbrowse/commit/eebacea01205971c19a374cbcf2c...

30 changed files

  • A tests/data/hg19_formatted/tracks/knownGene/chr1/names.txt
  • A tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/EST/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.txt
  • A tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.txt
  • A tests/data/volvox_formatted_names/tracks/snps/ctgA/names.txt
  • R tests/data/hg19_formatted/tracks/knownGene/chr1/names.json
  • R tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/EST/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.json
  • R tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.json
  • R tests/data/volvox_formatted_names/tracks/snps/ctgA/names.json
  • M bin/generate-names.pl
  • M src/perl5/NameHandler.pm
  • M tests/perl_tests/biodb-to-json.pl.t
  • M tests/perl_tests/flatfile-to-json.pl.t