Commits for markd

v428_preview2 to v428_base (2022-03-07 to 2022-03-14) v428

c6eed4550b6684cc7cde7779b9084a72573b5d83 Fri Mar 11 19:54:00 2022 -0800

• added ability to read ascii version of bigRmskAlign files
  • src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c - lines changed 69, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/hg38BigRmskTest.psl - lines changed 759, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/hg38.dfam_3.5.bigRmskIn - lines changed 997, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 5, context: html, text, full: html, text

0192d4b02dfdb61e29f71ab65340876d95d7af7a Sat Mar 12 23:32:19 2022 -0800

• have pslToBigPsl check for FASTA sequence length not matching PSL instead of having browser generate an error
  • src/hg/utils/pslToBigPsl/pslToBigPsl.c - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/input/MamRep605b.fa - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/input/MamRep605b.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslToBigPsl/tests/makefile - lines changed 5, context: html, text, full: html, text

56cfd7a79faa415392733aab06c016139e59a350 Sun Mar 13 09:47:25 2022 -0700

• test cases was actually Dfam 3.3
  • src/hg/utils/rmskAlignToPsl/tests/input/hg38.dfam_3.3.bigRmskIn - lines changed 997, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/hg38.dfam_3.5.bigRmskIn - lines changed 997, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 1, context: html, text, full: html, text

57d31ee9aede2bf610907285b05af8d9cbfe9bec Sun Mar 13 10:45:03 2022 -0700

• added ability to override incorrect sizes often found in RepeatMaster alignments
  • src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.bigRmskIn - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.sizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 5, context: html, text, full: html, text

661558a587c48930ceb19f3baa526c78d236f8d8 Sun Mar 13 10:49:48 2022 -0700

• fixed expected output
  • src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 3, context: html, text, full: html, text

e3828b90be3c817778a057af993f236bb5f9753b Sun Mar 13 11:07:35 2022 -0700

• fixed repeat counts
  • src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/hg38BigRmskTest.psl - lines changed 759, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/hg38Test.psl - lines changed 60, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/mm39ProbTest.psl - lines changed 10, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/mm39Test.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 4, context: html, text, full: html, text

f39d46885edb7bfab12a10158d13895a5010d2ff Sun Mar 13 11:21:26 2022 -0700

• fixed shell check for command that should have failed
  • src/hg/utils/pslToBigPsl/tests/makefile - lines changed 1, context: html, text, full: html, text

d99300bbd4e6250c0a72144745b3383a973adb14 Sun Mar 13 12:32:04 2022 -0700

• drop querys not in repSizes file rather than generate an error
  • src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c - lines changed 32, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/expected/wrongSizeTest.out - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.bigRmskIn - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 2, context: html, text, full: html, text

015db67f25bdbaffebb795b6e952c405f15e1e23 Sun Mar 13 14:10:06 2022 -0700

• premature commit of -repSizes, this really made things worse; back out
  • src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c - lines changed 73, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.bigRmskIn - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/input/wrongSize.sizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/rmskAlignToPsl/tests/makefile - lines changed 7, context: html, text, full: html, text