Commits for markd

v404_preview to v404_preview2 (2020-08-31 to 2020-09-07) v404

03fcdcc33cd21dad46aa78556cdb1d87ce37f144 Mon Aug 31 12:17:03 2020 -0700

• make gencodeV35Attrs more compatible with older tables
  • src/hg/inc/gencodeAttrs.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gencodeAttrs.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeAttrs.c - lines changed 55, context: html, text, full: html, text
  • src/hg/lib/gencodeAttrs.sql - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.attrs - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.attrs - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.attrs - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.attrs - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.attrs - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.attrs - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.attrs - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.attrs - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.attrs - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv - lines changed 12, context: html, text, full: html, text

ab38adb3e68ab9cf4c53d9b0df0ebf46f51ca999 Fri Sep 4 11:31:15 2020 -0700

• added bigGenePredToGenePred command
  • src/hg/utils/bigGenePredToGenePred/bigGenePredToGenePred.c - lines changed 50, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/tests/expected/basicTest.gp - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/tests/input/basic.bigGpIn - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/tests/input/hg38.sizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/tests/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text

34f3d96c4108f41b2bf73d72dbb5a95302c28b09 Fri Sep 4 20:18:49 2020 -0700

• removed option that was not actually used (I think this was my bad)
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 1, context: html, text, full: html, text