Commits for angie

v366_base to v367_preview (2018-05-29 to 2018-06-04) v367

81b2ee7407e5916847893c4851b38e0788efe728 Wed May 30 15:07:16 2018 -0700

• LRG mappings to the reference genomes used to always span the entire LRG, but they don't anymore; there may be one mapping that spans the entire LRG and another mapping that spans only part of it. Instead of assuming that lrgStart is 0 and lrgEnd is size, detect if they're not, and in that case bundle lrgStart and lrgEnd into the name field and parse back out when making PSL. sorta refs #13359 #17877
  • src/hg/lib/lrg.c - lines changed 48, context: html, text, full: html, text
  • src/hg/utils/automation/parseLrgXml.pl - lines changed 12, context: html, text, full: html, text

b55093589f69c02a2bd605a3334758d02aecc011 Wed May 30 17:44:47 2018 -0700

• Update LRG process to support alt haplotypes and patches. refs #18853
  • src/hg/makeDb/doc/hg19.txt - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/parseLrgXml.pl - lines changed 42, context: html, text, full: html, text