Commits for markd

v405_base to v406_preview (2020-10-05 to 2020-10-12) v406

dddc3258aec53ba33f27a2233816cc02a42b940d Wed Sep 30 12:41:38 2020 -0700

• refactor to simplified code in prep for fixing minOverlapping functionality
  • src/hg/geneBounds/clusterGenes/clusterGenes.c - lines changed 113, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingBasesTest.gl - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingCdsBasesTest.gl - lines changed 3, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/input/minOverlapCases.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/makefile - lines changed 9, context: html, text, full: html, text

f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700

• replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
  • src/hg/geneBounds/clusterGenes/clusterGenes.c - lines changed 154, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesCdsTest.gl - lines changed 5, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesTest.gl - lines changed 5, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingBasesTest.gl - lines changed 3, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingCdsBasesTest.gl - lines changed 3, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/input/minOverlapCases.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/input/overlapCases.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/input/smallOverlap.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/makefile - lines changed 9, context: html, text, full: html, text

9debf7ab57d1bccb620f13fa1ba81a0a9434211c Mon Oct 5 17:40:32 2020 -0700

• remove -minOverlappingBases rather than map it to the new option, since the behavior is significantly different enough than the intended old behavior that is is better to fail
  • src/hg/geneBounds/clusterGenes/clusterGenes.c - lines changed 8, context: html, text, full: html, text