File Changes for angie

v351_base to v352_preview (2017-06-26 to 2017-07-03) v352

• src/hg/inc/hgHgvs.h
  • lines changed 13, context: html, text, full: html, text
    e6e8263c1a4a85000be7cc4df0797d75dceba589 Fri Jun 30 09:51:18 2017 -0700
    Noncoding introns were not being mapped to the genome correctly, hgvsTranscriptToZeroBasedHalfOpen had a fencepost error for upstream/downstream and mapToDeletion was using q coords instead of t coords for upstream/downstream, doh! helpful testcase: NR_111987:n.-1 . fixes #19702 note-1.
• src/hg/lib/hgHgvs.c
  • lines changed 121, context: html, text, full: html, text
    a476f750f106fbcde8fedeb6488389d728f46396 Thu Jun 29 11:26:34 2017 -0700
    Oops, HGVS n. terms can have intron offsets too (like c. except for no UTR [-*] indicators). fixes #19702
  • lines changed 47, context: html, text, full: html, text
    e6e8263c1a4a85000be7cc4df0797d75dceba589 Fri Jun 30 09:51:18 2017 -0700
    Noncoding introns were not being mapped to the genome correctly, hgvsTranscriptToZeroBasedHalfOpen had a fencepost error for upstream/downstream and mapToDeletion was using q coords instead of t coords for upstream/downstream, doh! helpful testcase: NR_111987:n.-1 . fixes #19702 note-1.
  • lines changed 5, context: html, text, full: html, text
    0926946a1fed476484b175c2c7ce40de2b4f4bf9 Fri Jun 30 10:44:46 2017 -0700
    Prevent mapping warning (e.g. ref mismatch) from causing us to error out after parsing changes.
  • lines changed 67, context: html, text, full: html, text
    1fd5528b8d1ad70d0858fa650e0936a2102cfd0e Fri Jun 30 13:34:00 2017 -0700
    HGVS search was broken for double-sided gaps, i.e. messed up assembly regions where the alignment has to skip over transcript bases. Added pslFromGap to handle it. pslTransMap was already handling cases in which one end of a seach term was skipped but the other wasn't. fixes #19711
• src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
  • lines changed 1, context: html, text, full: html, text
    e6e8263c1a4a85000be7cc4df0797d75dceba589 Fri Jun 30 09:51:18 2017 -0700
    Noncoding introns were not being mapped to the genome correctly, hgvsTranscriptToZeroBasedHalfOpen had a fencepost error for upstream/downstream and mapToDeletion was using q coords instead of t coords for upstream/downstream, doh! helpful testcase: NR_111987:n.-1 . fixes #19702 note-1.
• src/utils/qa/weeklybld/summaryEmail.sh
  • lines changed 4, context: html, text, full: html, text
    6a5aa3d7b5ab245f727c0426761517a362430ab0 Mon Jun 26 12:33:09 2017 -0700
    Added --reverse to git command so that changes will be displayed in chronological order
  • lines changed 8, context: html, text, full: html, text
    50648ef2cbc18f5763d88c7ea6e17032b437321a Mon Jun 26 12:35:43 2017 -0700
    Changing variable name 'victim' to 'author' because it is more accurate.