File Changes for hiram
switch to commits view, user indexv294_preview to v294_preview2 (2013-12-16 to 2014-01-06) v294
- src/hg/blastToPsl/makefile
- lines changed 2, context: html, text, full: html, text
correctly cleaning tests/output directory refs #12260
- src/hg/makeDb/doc/hg38.txt
- lines changed 361, context: html, text, full: html, text
initial build and masking started refs #11682
- lines changed 227, context: html, text, full: html, text
add a cytoBand and the hg19 to hg38 difference track
- lines changed 159, context: html, text, full: html, text
working on genscan cpgIslands and PAR regions and added altLocations track refs #11681
- lines changed 199, context: html, text, full: html, text
documenting trf procedure refs #11681
- src/hg/makeDb/hgLoadOut/hgLoadOut.c
- lines changed 2, context: html, text, full: html, text
can also eliminate repEnd<0 bad records refs #11681
- src/hg/makeDb/trackDb/human/hg38/altLocations.html
- lines changed 6, context: html, text, full: html, text
adding altLocations and hg38ContigDiff track descriptions refs #11681
- src/hg/makeDb/trackDb/human/hg38/description.html
- lines changed 63, context: html, text, full: html, text
hg38 ready to view refs #11681
- src/hg/makeDb/trackDb/human/hg38/gap.html
- lines changed 34, context: html, text, full: html, text
hg38 ready to view refs #11681
- src/hg/makeDb/trackDb/human/hg38/gold.html
- lines changed 38, context: html, text, full: html, text
hg38 ready to view refs #11681
- src/hg/makeDb/trackDb/human/hg38/hg38ContigDiff.html
- lines changed 38, context: html, text, full: html, text
adding altLocations and hg38ContigDiff track descriptions refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html
- lines changed 105, context: html, text, full: html, text
adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html
- lines changed 125, context: html, text, full: html, text
adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 8, context: html, text, full: html, text
hg38 ready to view refs #11681
- lines changed 54, context: html, text, full: html, text
adding various repeat masker tracks and ctgPos2 refs #11681
- lines changed 15, context: html, text, full: html, text
add correct search rules for gold and ctgPos2 tracks refs #11681
- lines changed 16, context: html, text, full: html, text
adding scaffolds track and rmskBlastn and rmskGenbank description pages refs #11681
- lines changed 9, context: html, text, full: html, text
adding analysisGap refs #11681
- lines changed 1, context: html, text, full: html, text
correct url variable for ctgPos2 refs #11681
- lines changed 11, context: html, text, full: html, text
adding the hg19 to hg38 difference track refs #11681
- lines changed 28, context: html, text, full: html, text
adding hmmerUnique crossMatchUnique and altLocations tracks refs #11681
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
hg38 ready to view refs #11681
- src/hg/makefile
- lines changed 1, context: html, text, full: html, text
adding mouseStuff to the test target refs #12260
- src/hg/mouseStuff/axtChain/axtChain.c
- lines changed 1, 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/tests/expected/newStyleLastz.chain
- lines changed 115, 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/oldStyleBlastz.chain
- lines changed 106, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- src/hg/mouseStuff/axtChain/tests/input/hg19.chrM.2bit
- lines changed 0, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/hg19.chrM.fa
- lines changed 333, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- lines changed 333, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.Q.txt
- lines changed 20, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.axt
- lines changed 17, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- lines changed 17, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.axt.gz
- lines changed 0, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/newStyleLastz.psl
- lines changed 14, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.Q.txt
- lines changed 6, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.axt
- lines changed 8, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- lines changed 8, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.axt.gz
- lines changed 0, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/oldStyleBlastz.psl
- lines changed 5, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/susScr3.chrM.2bit
- lines changed 0, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/input/susScr3.chrM.fa
- lines changed 334, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- lines changed 334, context: html, text, full: html, text
packing input data and adding other tests refs #12260
- src/hg/mouseStuff/axtChain/tests/makefile
- lines changed 27, context: html, text, full: html, text
testing old blastz vs. new lastz scoring matrix file scheme formats refs #12260
- lines changed 56, context: html, text, full: html, text
silence the test output and add other test options refs #12260
- lines changed 2, context: html, text, full: html, text
correct gz input for the other test cases refs #12260
- src/hg/mouseStuff/lavToAxt/lavToAxt.c
- lines changed 2, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/expected/crea.axt
- lines changed 4, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- src/hg/mouseStuff/lavToAxt/tests/expected/newStyleLastz.axt
- lines changed 8, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/expected/oldStyleBlastz.axt
- lines changed 8, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/fa/hCreaGeno.fa
- lines changed 100, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- src/hg/mouseStuff/lavToAxt/tests/fa/mCreaGeno.fa
- lines changed 114, 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/input/hCreaGeno.2bit
- lines changed 0, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/hg19.chrM.2bit
- lines changed 0, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/hg19.chrM.fa
- lines changed 333, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/mCreaGeno.2bit
- lines changed 0, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/newStyleLastz.Q.txt
- lines changed 20, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/newStyleLastz.lav
- lines changed 128, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/oldStyleBlastz.Q.txt
- lines changed 6, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/oldStyleBlastz.lav
- lines changed 128, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/susScr3.chrM.2bit
- lines changed 0, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- src/hg/mouseStuff/lavToAxt/tests/input/susScr3.chrM.fa
- lines changed 334, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- src/hg/mouseStuff/lavToAxt/tests/makefile
- lines changed 23, context: html, text, full: html, text
adding tests to work with new style lastz parameter file formats refs #12260
- lines changed 37, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- lines changed 2, context: html, text, full: html, text
adding additional test and reviving ancient test refs #12260
- 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/lavToPsl/lavToPsl.c
- lines changed 49, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- lines changed 24, context: html, text, full: html, text
add pslFree and bedFree plus remove old cruft refs #12206
- src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.bed
- lines changed 5, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/expected/newStyleLastz.psl
- lines changed 5, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.bed
- lines changed 5, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/expected/oldStyleBlastz.psl
- lines changed 5, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/input/newStyleLastz.lav
- lines changed 128, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/input/oldStyleBlastz.lav
- lines changed 128, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/makefile
- lines changed 26, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- src/hg/mouseStuff/lavToPsl/tests/output/oldStyleBlastz.psl
- lines changed 5, context: html, text, full: html, text
adding tests and fixup bed output that never worked refs #12206
- lines changed 5, context: html, text, full: html, text
mistaken addition removed refs @12206
- src/hg/mouseStuff/makefile
- lines changed 7, context: html, text, full: html, text
adding mouseStuff to the test target refs #12260
- lines changed 4, context: html, text, full: html, text
honor the clean target and get all subdirs cleaned
- src/hg/mouseStuff/netToAxt/tests/makefile
- lines changed 2, context: html, text, full: html, text
do not need to see the information output from the command
- src/hg/utils/automation/HgAutomate.pm
- lines changed 27, context: html, text, full: html, text
fixup the default clusters and workhorse lists for the ku environment refs #11681
- src/hg/utils/automation/blastz-run-ucsc
- lines changed 64, 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/doBlastzChainNet.pl
- lines changed 75, 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/doRepeatMasker.pl
- lines changed 1, context: html, text, full: html, text
save the bad records result refs #11681
- src/hg/utils/automation/doSimpleRepeat.pl
- lines changed 5, context: html, text, full: html, text
avoid attempting to lift zero length files which is an error refs #11681
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 6, 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/phyloTrees/120way.commonNames.nh
- lines changed 120, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/120way.nh
- lines changed 120, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/120way.scientificNames.nh
- lines changed 120, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/commonNames.sh
- lines changed 5, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
- lines changed 6, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/makefile
- lines changed 7, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/placentals.txt
- lines changed 11, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/scientificNames.sh
- lines changed 9, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/hg/utils/phyloTrees/vertebrates.txt
- lines changed 17, context: html, text, full: html, text
adding to 113way: balAcu1 bubBub1 calMil1 cotJap1 letCam1 lipVex1 perBai1 refs #10272
- src/makefile
- lines changed 1, context: html, text, full: html, text
correctly clean parasol directory during clean target refs #9104
- src/utils/bigWigCat/tests/makefile
- lines changed 7, context: html, text, full: html, text
correctly using destbindir for binary access
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
v294 preview2 refs #12191
- src/utils/wigToBigWig/tests/makefile
- lines changed 1, context: html, text, full: html, text
correct use of destbindir binary
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