Commits for markd

v462_preview2 to v462_base (2024-03-04 to 2024-03-11) v462

cf2ea277055c7881254552745ce3e38e0d23f9a5 Mon Mar 4 20:36:11 2024 -0800

• import of GENCODE V46 prerelease
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.html - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.ra - lines changed 247, context: html, text, full: html, text

ba39846fb30a64ba6df41c0aae781915ddf61c80 Mon Mar 4 22:15:06 2024 -0800

• import of GENCODE VM35
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM35.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM35.ra - lines changed 247, context: html, text, full: html, text

2c3bfb6253d13a518eb2f3697d62224bdfa4aa54 Thu Mar 7 21:01:21 2024 -0800

• add new test cases that shows that bamToPsl is broken; restructure tests to match the rest
  • src/utils/bamToPsl/tests/chr9.NM_020469.2.blat.bam - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/bamToPsl/tests/expected/test1.psl - lines changed 11, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/expected/test2.psl - lines changed 14, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/expectedOut.psl - lines changed 11, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/input/chr9.NM_020469.2.blat.bam - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/bamToPsl/tests/input/multimap.qsizes - lines changed 1, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/input/multimap.sam - lines changed 28, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/makefile - lines changed 27, context: html, text, full: html, text

4f600be98e2fe9e71637a704978a596029849ef4 Thu Mar 7 21:43:58 2024 -0800

• disable check of PSL, since bamToPsl is broken
  • src/utils/bamToPsl/tests/makefile - lines changed 2, context: html, text, full: html, text

bd19d0f0854ea7e27017395d96715b61071b3391 Thu Mar 7 22:49:24 2024 -0800

• restructure code to make it easier to modify and then simplified by remove fasta checksum complexity checks that were added because of a missunderstanding about how supplemental alignments were represented
  • src/utils/bamToPsl/bamToPsl.c - lines changed 104, context: html, text, full: html, text

49d67ce8f1bd5e1f0b5a5ae1133a8ffe507c50eb Thu Mar 7 22:52:20 2024 -0800

• added test case for fasta output
  • src/utils/bamToPsl/tests/expected/test2.fa - lines changed 3164, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/makefile - lines changed 2, context: html, text, full: html, text

474b9ac55dcb8e3c4cc56b00d52bd210b7989038 Thu Mar 7 22:59:45 2024 -0800

• create PSLs for supplementary alignments that correct represent the query alignment. RM: 33209
  • src/inc/bamFile.h - lines changed 6, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 18, context: html, text, full: html, text
  • src/utils/bamToPsl/bamToPsl.c - lines changed 3, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/expected/test2.psl - lines changed 8, context: html, text, full: html, text
  • src/utils/bamToPsl/tests/makefile - lines changed 1, context: html, text, full: html, text

2322474c8ecc8f865350c14ea60a464248bd5c84 Fri Mar 8 00:02:10 2024 -0800

• make pslToBigPsl help slightly more helpful
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 1, context: html, text, full: html, text