Commits for braney

v376_preview to v376_preview2 (2018-12-17 to 2019-01-07) v376

e6e7df9527a71c876c262fdc42d16e1af0eef013 Wed Dec 26 07:19:27 2018 -0800

• remove xenoMrna from rn3 because blat is blowing up on it
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text

f698da27426bf0aa389780675b4238d0fb8f249b Wed Dec 26 11:51:06 2018 -0800

• oops... disable genbank xenoMrna track for rn3
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 2, context: html, text, full: html, text

9744b1d0f27d7dcea4599b03e4b15a9e9970238a Thu Jan 3 13:09:50 2019 -0800

• blast tabs tables should index the entire query #2273
  • src/hg/makeDb/hgLoadBlastTab/hgLoadBlastTab.c - lines changed 1, context: html, text, full: html, text

3f97f523805e249626accd3c855ae2ed841b7d34 Thu Jan 3 15:29:44 2019 -0800

• use full query for index #22713
  • src/hg/near/hgExpDistance/hgExpDistance.c - lines changed 2, context: html, text, full: html, text

e0260964813a12bd5a33cbd662ae27f029369c3a Thu Jan 3 15:51:09 2019 -0800

• use all of query in index #22713
  • src/hg/near/hgNetDist/hgLoadNetDist.c - lines changed 1, context: html, text, full: html, text

9466f0e71913fd917ee6c919a8a8b31edd59a9c0 Thu Jan 3 16:34:29 2019 -0800

• use all of query for index #22713
  • src/hg/lib/pslReader.c - lines changed 1, context: html, text, full: html, text

c0a6048e07b4cae079738ca5b3cb076493dbd19e Fri Jan 4 10:00:37 2019 -0800

• modify some knownGene SQL files to use full query for index #22713
  • src/hg/lib/knownCanonical.sql - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/knownTo.sql - lines changed 2, context: html, text, full: html, text

b4098c773b944482ec48818e63b1518a90660d35 Fri Jan 4 11:07:36 2019 -0800

• use NCBI RefSeq instead of UCSC RefSeq for the CDS FASTA files
  • src/hg/makeDb/doc/hg38/multiz100way.txt - lines changed 8, context: html, text, full: html, text

3315cb5c5cb6380b15c17f7b9531dc4f33bdee49 Fri Jan 4 11:08:41 2019 -0800

• add a little note about the creation of knownBlastTab
  • src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes19.sh - lines changed 2, context: html, text, full: html, text

6096ae468c0bec9a0f6818d1a12136d9987ef3f1 Sun Jan 6 11:37:29 2019 -0800

• allocate some memory out of the heap instead of the stack, which was overflowing on huge sequences
  • src/hg/pslCDnaFilter/localNearBestFilter.c - lines changed 2, context: html, text, full: html, text

6b6e1c15a73e157b9f811f11e7c7d2488e3cb435 Mon Jan 7 07:53:51 2019 -0800

• oops, forgot to free newly allocated memory
  • src/hg/pslCDnaFilter/localNearBestFilter.c - lines changed 1, context: html, text, full: html, text