Commits for kent

v431_preview2 to v431_base (2022-05-09 to 2022-05-16) v431

9baf8d2adf6de7a935ae05fe74246a8eb725bf22 Wed May 11 13:10:43 2022 -0700

• First cut of bedGraphToWig
  • src/utils/bedGraphToWig/bedGraphToWig.c - lines changed 135, context: html, text, full: html, text
  • src/utils/bedGraphToWig/err1.bed - lines changed 6, context: html, text, full: html, text
  • src/utils/bedGraphToWig/err2.bed - lines changed 6, context: html, text, full: html, text
  • src/utils/bedGraphToWig/err3.bed - lines changed 6, context: html, text, full: html, text
  • src/utils/bedGraphToWig/fixed.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedGraphToWig/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/bedGraphToWig/var.bed - lines changed 5, context: html, text, full: html, text

0957695666775bee81510336f88a2b9dbbef9203 Thu May 12 06:14:05 2022 -0700

• ref #29416 - Making it so that all the genes of a given name (but just for a particular version of genes) are output in the mapping.bed file, rather than just the most recent one added to the hash.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 26, context: html, text, full: html, text

7a5533f3131b50e00f7568767cf837c4c418b6a0 Thu May 12 06:40:55 2022 -0700

• Outputting all genes with same name so get refSeq on both alts and main chromosomes.
  • src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c - lines changed 3, context: html, text, full: html, text

2af681b48db9f2763dc35912ecd267a8bae96d8b Thu May 12 08:37:32 2022 -0700

• Making it take most recent GENCODE by preference when -targetDb option is set again.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 7, context: html, text, full: html, text