Commits for hiram

v294_preview to v294_preview2 (2013-12-16 to 2014-01-06) v294

• correctly clean parasol directory during clean target refs #9104
  • src/makefile - lines changed 1, context: html, text, full: html, text
• testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
  • src/hg/mouseStuff/axtChain/tests/expected/newStyleLastz.chain - lines changed 115, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/expected/oldStyleBlastz.chain - lines changed 106, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/hg19.chrM.fa - lines changed 333, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.Q.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.axt - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.Q.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.axt - lines changed 8, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/susScr3.chrM.fa - lines changed 334, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/makefile - lines changed 27, context: html, text, full: html, text
• adding mouseStuff to the test target refs #12260
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/makefile - lines changed 7, context: html, text, full: html, text
• adding tests to work with new style lastz parameter file formats refs #12260
  • src/hg/mouseStuff/lavToAxt/lavToAxt.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/expected/newStyleLastz.axt - lines changed 8, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/expected/oldStyleBlastz.axt - lines changed 8, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/hg19.chrM.fa - lines changed 333, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/newStyleLastz.Q.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/newStyleLastz.lav - lines changed 128, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/oldStyleBlastz.Q.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/oldStyleBlastz.lav - lines changed 128, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/susScr3.chrM.fa - lines changed 334, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/makefile - lines changed 23, context: html, text, full: html, text
• correctly cleaning tests/output directory refs #12260
  • src/hg/blastToPsl/makefile - lines changed 2, context: html, text, full: html, text
• packing input data and adding other tests refs #12260
  • src/hg/mouseStuff/axtChain/tests/input/hg19.chrM.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/axtChain/tests/input/hg19.chrM.fa - lines changed 333, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.axt - lines changed 17, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.axt.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.psl - lines changed 14, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.axt - lines changed 8, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.axt.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/mouseStuff/axtChain/tests/input/susScr3.chrM.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/axtChain/tests/input/susScr3.chrM.fa - lines changed 334, context: html, text, full: html, text
• silence the test output and add other test options refs #12260
  • src/hg/mouseStuff/axtChain/tests/makefile - lines changed 56, context: html, text, full: html, text
• add usage note warning about trying to use gzipped fasta file input does not work refs #12260
  • src/hg/mouseStuff/axtChain/axtChain.c - lines changed 1, context: html, text, full: html, text
• correct gz input for the other test cases refs #12260
  • src/hg/mouseStuff/axtChain/tests/makefile - lines changed 2, context: html, text, full: html, text
• adding additional test and reviving ancient test refs #12260
  • src/hg/mouseStuff/lavToAxt/tests/expected/crea.axt - lines changed 4, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/fa/hCreaGeno.fa - lines changed 100, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/fa/mCreaGeno.fa - lines changed 114, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/input/hCreaGeno.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToAxt/tests/input/hg19.chrM.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToAxt/tests/input/mCreaGeno.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToAxt/tests/input/susScr3.chrM.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToAxt/tests/makefile - lines changed 37, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/tests/test - lines changed 11, context: html, text, full: html, text
• adding additional test and reviving ancient test refs #12260
  • src/hg/mouseStuff/lavToAxt/tests/input/crea.lav - lines changed 188, context: html, text, full: html, text
• adding additional test and reviving ancient test refs #12260
  • src/hg/mouseStuff/lavToAxt/tests/makefile - lines changed 2, context: html, text, full: html, text
• adding tests and fixup bed output that never worked refs #12206
  • src/hg/mouseStuff/lavToPsl/lavToPsl.c - lines changed 49, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/input/newStyleLastz.lav - lines changed 128, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/input/oldStyleBlastz.lav - lines changed 128, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/makefile - lines changed 26, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/output/oldStyleBlastz.psl - lines changed 5, context: html, text, full: html, text
• correct use of destbindir binary
  • src/utils/wigToBigWig/tests/makefile - lines changed 1, context: html, text, full: html, text
• correctly using destbindir for binary access
  • src/utils/bigWigCat/tests/makefile - lines changed 7, context: html, text, full: html, text
• add pslFree and bedFree plus remove old cruft refs #12206
  • src/hg/mouseStuff/lavToPsl/lavToPsl.c - lines changed 24, context: html, text, full: html, text
• mistaken addition removed refs @12206
  • src/hg/mouseStuff/lavToPsl/tests/output/oldStyleBlastz.psl - lines changed 5, context: html, text, full: html, text
• honor the clean target and get all subdirs cleaned
  • src/hg/mouseStuff/makefile - lines changed 4, context: html, text, full: html, text
• do not need to see the information output from the command
  • src/hg/mouseStuff/netToAxt/tests/makefile - lines changed 2, context: html, text, full: html, text
• adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
  • src/hg/utils/phyloTrees/120way.commonNames.nh - lines changed 120, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/120way.nh - lines changed 120, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/120way.scientificNames.nh - lines changed 120, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 17, context: html, text, full: html, text
• hg38 ready to view refs #11681
  • src/hg/makeDb/trackDb/human/hg38/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gap.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gold.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• initial build and masking started refs #11682
  • src/hg/makeDb/doc/hg38.txt - lines changed 361, context: html, text, full: html, text
• adding various repeat masker tracks and ctgPos2 refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 54, context: html, text, full: html, text
• add correct search rules for gold and ctgPos2 tracks refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 15, context: html, text, full: html, text
• adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
  • src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html - lines changed 125, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 16, context: html, text, full: html, text
• adding analysisGap refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 9, context: html, text, full: html, text
• correct url variable for ctgPos2 refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
• add a cytoBand and the hg19 to hg38 difference track
  • src/hg/makeDb/doc/hg38.txt - lines changed 227, context: html, text, full: html, text
• adding the hg19 to hg38 difference track refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 11, context: html, text, full: html, text
• can also eliminate repEnd<0 bad records refs #11681
  • src/hg/makeDb/hgLoadOut/hgLoadOut.c - lines changed 2, context: html, text, full: html, text
• adding hmmerUnique crossMatchUnique and altLocations tracks refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 28, context: html, text, full: html, text
• working on genscan cpgIslands and PAR regions and added altLocations track refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 159, context: html, text, full: html, text
• adding altLocations and hg38ContigDiff track descriptions refs #11681
  • src/hg/makeDb/trackDb/human/hg38/altLocations.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hg38ContigDiff.html - lines changed 38, context: html, text, full: html, text
• fixup the default clusters and workhorse lists for the ku environment refs #11681
  • src/hg/utils/automation/HgAutomate.pm - lines changed 27, context: html, text, full: html, text
• can now use a package of 2bit sequences for the query to modern lastz versions refs #11681
  • src/hg/utils/automation/blastz-run-ucsc - lines changed 64, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 75, context: html, text, full: html, text
• save the bad records result refs #11681
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 1, context: html, text, full: html, text
• avoid attempting to lift zero length files which is an error refs #11681
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 5, context: html, text, full: html, text
• add type pre draft to recognize in an AGP file and fixup the split threshold to avoid 1,000 directories refs #11681
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 6, context: html, text, full: html, text
• documenting trf procedure refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 199, context: html, text, full: html, text
• v294 preview2 refs #12191
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text