Commits for angie

v307_preview2 to v307_base (2014-10-06 to 2014-10-13) v307

• Built hg17ToHg38 liftOver chains (requested by DGV contributor Jeff MacDonald).
  • src/hg/makeDb/doc/hg17.txt - lines changed 15, context: html, text, full: html, text
• Two of the three alt sequences for chrX are in PAR1; the other doesn'toverlap either par. Added two chrX_*_alt...PAR1 entries to the par table.
  
  • src/hg/makeDb/doc/hg38.txt - lines changed 39, context: html, text, full: html, text
• Built hg16ToHg38 liftOver chains (requested by DGV contributor Jeff MacDonald).
  • src/hg/makeDb/doc/hg16.txt - lines changed 15, context: html, text, full: html, text
• Regenerated most snp141* tables and snp-masked sequences after Matt foundthat MultipleAlignments was assigned incorrectly for a region of PAR1
  that happens to have a couple alt sequences in hg38. In an earlier
  commit I added the chrX_*alts to the par table; then in this commit I
  re-ran the SNP pipeline from snpnNcbiToUcsc (which uses par.bed) onward.
  I also turned a sequence of 3 45-minute commands into a 10-minute cluster
  job followed by one 45-minute sort.
  refs #13309
  
  • src/hg/makeDb/doc/hg38.txt - lines changed 150, context: html, text, full: html, text