Commits for hiram

v321_preview2 to v321_base (2015-08-17 to 2015-08-24) v321

• adding track chainNets for hetBac1 ancCey1 necAme1 ascSuu1 priExs1 and loaLoa1 refs #15209
  
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 306, context: html, text, full: html, text
• adding NCBI gene track definition refs #15209
  
  • src/hg/makeDb/trackDb/worm/ncbiGenes.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/trackDb.ra - lines changed 18, context: html, text, full: html, text
• Added ascSuu1 - Pig roundworm/Ascaris suum refs #15209
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• fixup ascSuu1 definitions for better results refs #15209
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 11, context: html, text, full: html, text
• fixup to naming scheme of hg38 refs #15524
  
  • src/hg/stsMarkers/findAccession.pl - lines changed 15, context: html, text, full: html, text
• photo from CDC refs #15209
  
  • src/hg/htdocs/images/Brugia_malayi.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• updated photo refs #15209
  
  • src/hg/makeDb/trackDb/worm/bruMal2/description.html - lines changed 1, context: html, text, full: html, text
• rerun assembly with wolbachia sequence and add correct photo refs #15209
  
  • src/hg/makeDb/doc/worms/bruMal2.txt - lines changed 92, context: html, text, full: html, text
• adding photo for burXyl1 from USDA photo refs #15209
  
  • src/hg/htdocs/images/Bursaphelenchus_xylophilus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding correct photo refs #15209
  
  • src/hg/makeDb/trackDb/worm/burXyl1/description.html - lines changed 4, context: html, text, full: html, text
• correct image size in the href refs #15209
  
  • src/hg/makeDb/trackDb/worm/burXyl1/description.html - lines changed 2, context: html, text, full: html, text
• adding photo for melInc from USDA images refs #15209
  
  • src/hg/htdocs/images/Meloidogyne_incognita.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct photo from USDA refs #15209
  
  • src/hg/makeDb/trackDb/worm/melInc1/description.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/melInc2/description.html - lines changed 4, context: html, text, full: html, text
• adding image for haeCon from CSIRO refs #15209
  
  • src/hg/htdocs/images/Haemonchus_contortus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct photo from CSIRO refs #15209
  
  • src/hg/makeDb/trackDb/worm/haeCon1/description.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/haeCon2/description.html - lines changed 4, context: html, text, full: html, text
• adding correct photo from CSIRO refs #15209
  
  • src/hg/makeDb/doc/worms/haeCon2.txt - lines changed 17, context: html, text, full: html, text
• photo for panRed1 from wikimedia commons refs #15209
  
  • src/hg/htdocs/images/Panagrellus_redivivus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct photo from WikiMedia Commons refs #15209
  
  • src/hg/makeDb/trackDb/worm/panRed1/description.html - lines changed 4, context: html, text, full: html, text
• adding correct photo from WikiMedia Commons refs #15209
  
  • src/hg/makeDb/doc/worms/panRed1.txt - lines changed 19, context: html, text, full: html, text
• adding Pristionchus photo from Max Planck Institute refs #15209
  
  • src/hg/htdocs/images/Pristionchus_exspectatus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding photo from Max Planck Institute refsw #15209
  
  • src/hg/makeDb/trackDb/worm/priExs1/description.html - lines changed 3, context: html, text, full: html, text
• adding a Pristionchus photo from Max Planck Institute refs #15209
  
  • src/hg/makeDb/doc/worms/priExs1.txt - lines changed 11, context: html, text, full: html, text
• Added ascSuu1 - Ascaris suum/Pig roundworm refs #15209
  
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
• done with genbank run refs #15209
  
  • src/hg/makeDb/doc/worms/ascSuu1.txt - lines changed 57, context: html, text, full: html, text
• collected make doc from lastz runs refs #15209
  
  • src/hg/makeDb/doc/worms/lastz.ancCey1.txt - lines changed 812, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.ascSuu1.txt - lines changed 638, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.bruMal2.txt - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.burXyl1.txt - lines changed 348, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.caeAng2.txt - lines changed 1083, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.caeJap4.txt - lines changed 1197, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.caePb3.txt - lines changed 1368, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.caeRem4.txt - lines changed 1311, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.caeSp111.txt - lines changed 1140, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.caeSp51.txt - lines changed 1032, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.cb4.txt - lines changed 1254, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.dirImm1.txt - lines changed 290, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.haeCon2.txt - lines changed 696, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.hetBac1.txt - lines changed 986, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.loaLoa1.txt - lines changed 232, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.melHap1.txt - lines changed 464, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.melInc2.txt - lines changed 406, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.necAme1.txt - lines changed 754, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.oncVol1.txt - lines changed 116, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.panRed1.txt - lines changed 870, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.priExs1.txt - lines changed 580, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.priPac3.txt - lines changed 522, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.strRat2.txt - lines changed 928, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/lastz.triSpi1.txt - lines changed 58, context: html, text, full: html, text
• bring up to spec for hg38 stsMap build refs #15524
  
  • src/hg/pslFilterPrimers/pslFilterPrimers.c - lines changed 12, context: html, text, full: html, text
• update cloneEndbadEnds table load for BAC ends refs #13713
  
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 25, context: html, text, full: html, text
• Added priExs1 - P. exspectatus refs #15209
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text
• Added priExsNames - P. exspectatus refs #15209
  
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• better error messages instead of SegFault and can find no use for seqList refs #15899
  
  • src/hg/mouseStuff/axtChain/axtChain.c - lines changed 18, context: html, text, full: html, text
• update to correct /usr/bin/env perl invocation line refs #15524
  
  • src/hg/stsMarkers/combineSeqPrimerPos - lines changed 1, context: html, text, full: html, text
• done with stsMap track build refs #15524
  
  • src/hg/makeDb/doc/hg38/stsMap.txt - lines changed 294, context: html, text, full: html, text
• completed lastz runs for vicPac2 orcOrc1 speTri2 loxAfr3 hetGla2 felCat8 musFur1 dasNov3 panHod1 capHir1 triMan1 conCri1 echTel2 micMur2 refs #14560
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 194, context: html, text, full: html, text
• fix leaked in hg19 results into stsMap refs #15524
  
  • src/hg/makeDb/doc/hg38/stsMap.txt - lines changed 6, context: html, text, full: html, text
• v321 final build refs #15836
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v321
  
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text