Commits for markd

v460_preview2 to v460_base (2024-01-22 to 2024-01-29) v460

335d4c88dcce7148ccb0f6df4a18a2881b2075f7 Wed Jan 24 11:34:06 2024 -0800

• Check number of columns when reading auxillary tab files. This caused use of uninitialized memory, inserting garbage and ocassional newlines in BED file
  • src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c - lines changed 3, context: html, text, full: html, text

b4f6c6c609d1e6ff8f09c2f42795b1df05f31452 Wed Jan 24 20:42:01 2024 -0800

• try harder to find a more useful name for GFF3 records that don't follow the most common patterns. This are things like RefSeq IG segments and tRNAs that NHGRI had problems with
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 31, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/discontinuousTest.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/frameShiftTest.gp - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/geneTranscriptTest.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.attrs - lines changed 101, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.gp - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/minimalGenesTest.gp - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/multCdsOutOfExonTest.out - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs - lines changed 158, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.gp - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/noExonsTest.gp - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/input/noId.gff3 - lines changed 6, context: html, text, full: html, text

d8a01805f188894f0a2dbdbafefe3b522874fa28 Thu Jan 25 13:57:24 2024 -0800

• removed use of RefSeq standard_name in generating names, there are some cases were it contains long english phrase
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.attrs - lines changed 84, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/ncbiSegmentsTest.gp - lines changed 7, context: html, text, full: html, text