File Changes for angie

v348_base to v349_preview (2017-04-24 to 2017-05-01) v349

• src/hg/hgVai/hgVai.c
  • lines changed 18, context: html, text, full: html, text
    8ce7da98082db69f86314bf79d8f69978e008455 Fri Apr 28 16:43:36 2017 -0700
    hgVai was crashing when there was a new snpNNN table in the database but not yet in trackDb. Now make sure to use the latest SNPs track not just the latest table. refs #19272
• src/hg/inc/hdb.h
  • lines changed 2, context: html, text, full: html, text
    8ce7da98082db69f86314bf79d8f69978e008455 Fri Apr 28 16:43:36 2017 -0700
    hgVai was crashing when there was a new snpNNN table in the database but not yet in trackDb. Now make sure to use the latest SNPs track not just the latest table. refs #19272
• src/hg/js/hgVarAnnogrator.js
  • lines changed 3, context: html, text, full: html, text
    d9c3524816e461a40daeb695088fd6e3d65aa379 Fri Apr 28 14:09:50 2017 -0700
    Don't show loadingImage when user is saving to a file because then it never goes away. refs #19305
• src/hg/lib/hdb.c
  • lines changed 38, context: html, text, full: html, text
    8ce7da98082db69f86314bf79d8f69978e008455 Fri Apr 28 16:43:36 2017 -0700
    hgVai was crashing when there was a new snpNNN table in the database but not yet in trackDb. Now make sure to use the latest SNPs track not just the latest table. refs #19272
• src/hg/lib/hgHgvs.c
  • lines changed 64, context: html, text, full: html, text
    b1291b0928de2ce364c5335642acfc457110641e Mon Apr 24 14:08:18 2017 -0700
    When an HGVS term maps to a base that has been deleted from the reference genome, e.g. NM_020469.2(ABO):c.261= maps to a deleted base in hg19 & hg38, pslTransMap returns NULL, so we were failing to map it to any genomic location. Added mapToDeletion for this special case, so we can map to the zero-length region where the reference genome has a deleted base.
• src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
  • lines changed 1, context: html, text, full: html, text
    70f54565f755ee8d55105606220d7ebaf04d2133 Mon Apr 24 14:41:54 2017 -0700
    Strange consequence of last commit for test case: ncbiRefSeqPsl has only one mapping to an _alt. refSeqAli has mappings to both chr11 and chr11_alt. Previously, pslMap would return NULL for the _alt mapping due to NM_000218.2:c.1071 being deleted in the _alt, and so we would fall back on refSeqAli and get its chr11 mapping. But now we are able to map to the location of the deletion, we get the _alt mapping but not the chr11 mapping because we no longer fall back on refSeqAli.