Commits for hiram
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v281_base to v282_preview (2013-03-25 to 2013-04-02) v282
- add search rule for gold table refs #9812
- src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra - lines changed 19, context: html, text, full: html, text
- jerboa moved closer to mouse rat before squirrel and kangaroo rat refs #10272
- src/hg/utils/phyloTrees/97way.nh - lines changed 3, context: html, text, full: html, text
- restore distances to the same as they were in the mm10 60-way refs #10272
- src/hg/utils/phyloTrees/97way.nh - lines changed 23, context: html, text, full: html, text
- restore distances to the same as they were in the mm10 60-way refs #10272
- src/hg/utils/phyloTrees/97way.commonNames.nh - lines changed 77, context: html, text, full: html, text
- src/hg/utils/phyloTrees/97way.scientificNames.nh - lines changed 77, context: html, text, full: html, text
- src/hg/utils/phyloTrees/commonNames.sh - lines changed 1, context: html, text, full: html, text
- src/hg/utils/phyloTrees/scientificNames.sh - lines changed 1, context: html, text, full: html, text
- addes hg19 micMur1 swap for lift over refs #10485
- src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
- photo for amaVit1 browser, Tom MacKenzie, U.S. Fish and Wildlife Service www.fws.gov/caribbean/ES/Parrot-Gallery.html refs #10144
- src/hg/htdocs/images/Amazona_vittata.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- initial files from makeGenomeDb.pl refs #10144
- src/hg/makeDb/trackDb/birds/amaVit1/description.html - lines changed 63, context: html, text, full: html, text
- src/hg/makeDb/trackDb/birds/amaVit1/gap.html - lines changed 30, context: html, text, full: html, text
- src/hg/makeDb/trackDb/birds/amaVit1/gold.html - lines changed 33, context: html, text, full: html, text
- src/hg/makeDb/trackDb/birds/amaVit1/trackDb.ra - lines changed 8, context: html, text, full: html, text
- adding amaVit1 parrot to the build refs #10144
- src/hg/makeDb/trackDb/makefile - lines changed 2, context: html, text, full: html, text
- processing genbank unplaced scaffold assemblies into AGP and UCSC named fasta files, refs #10144
- src/hg/utils/automation/unplacedScaffolds.pl - lines changed 122, context: html, text, full: html, text
- prototype for new config.ra template creation, refs #10144
- src/hg/utils/automation/mkConfigRa.sh - lines changed 84, context: html, text, full: html, text
- correct usage message, refs #10144
- src/hg/utils/automation/mkConfigRa.sh - lines changed 29, context: html, text, full: html, text
- initial browser done, masking in progress, refs #10144
- src/hg/makeDb/doc/amaVit1.txt - lines changed 486, context: html, text, full: html, text
- NHGRI is changing their photo links refs #9812
- src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html - lines changed 1, context: html, text, full: html, text
- add notes about chromosome names refs #9812
- src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html - lines changed 26, context: html, text, full: html, text
- order the chrM contigs numerically refs #9812
- src/hg/makeDb/trackDb/gibbon/nomLeu3/description.html - lines changed 9, context: html, text, full: html, text
- cleanup and proper DESTDIR for refs #9104
- src/utils/faCat/makefile - lines changed 6, context: html, text, full: html, text
- done with masking, ready for genbank refs #10144
- src/hg/makeDb/doc/amaVit1.txt - lines changed 72, context: html, text, full: html, text
- per user request refs #10398
- src/hg/makeDb/doc/mm9.txt - lines changed 100, context: html, text, full: html, text
- src/hg/makeDb/doc/rn5.txt - lines changed 35, context: html, text, full: html, text
- adding some sanity to the makefiles with DESTDIR compile and install targets refs #9104
- src/utils/aNotB/makefile - lines changed 7, context: html, text, full: html, text
- src/utils/addCols/makefile - lines changed 11, context: html, text, full: html, text
- src/utils/aveCols/makefile - lines changed 16, context: html, text, full: html, text
- src/utils/bdfToGem/makefile - lines changed 7, context: html, text, full: html, text
- src/utils/bestThreshold/makefile - lines changed 18, context: html, text, full: html, text
- src/utils/cCp/makefile - lines changed 16, context: html, text, full: html, text
- broken compile refs #9104
- done with genscan and cpgIslandExt refs #10144
- src/hg/makeDb/doc/amaVit1.txt - lines changed 15, context: html, text, full: html, text
- protect nomLeu1 chain on public with the release tag and add Gibbon to the primate chain net description page
- src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
- reset default position slightly and add hg19 chain net swap procedure, refs #9812
- src/hg/makeDb/doc/nomLeu3.txt - lines changed 24, context: html, text, full: html, text
- testing new makefile organization refs #9104
- src/cdnaAli/ali2alx/makefile - lines changed 9, context: html, text, full: html, text
- src/utils/aNotB/makefile - lines changed 17, context: html, text, full: html, text
- src/utils/ave/makefile - lines changed 14, context: html, text, full: html, text
- src/utils/aveCols/makefile - lines changed 22, context: html, text, full: html, text
- src/utils/bedRemoveOverlap/makefile - lines changed 17, context: html, text, full: html, text
- src/utils/bestThreshold/makefile - lines changed 26, context: html, text, full: html, text
- src/utils/cCp/makefile - lines changed 22, context: html, text, full: html, text
- src/utils/faCat/makefile - lines changed 17, context: html, text, full: html, text
- src/utils/twoBitToFa/makefile - lines changed 15, context: html, text, full: html, text
- adding src/hg/utils link support with jkhgap and mysql libs libraries on conditional refs #9104
- adding src/hg/utils link support with jkhgap and mysql libs libraries on conditional refs #9104
- src/hg/utils/gapToLift/makefile - lines changed 17, context: html, text, full: html, text
- using new minimal makefile construction refs #9104
- src/cdnaAli/aliGlue/makefile - lines changed 12, context: html, text, full: html, text
- src/cdnaAli/binGood/makefile - lines changed 10, context: html, text, full: html, text
- src/cdnaAli/cdnaOff/makefile - lines changed 10, context: html, text, full: html, text
- src/cdnaAli/cluster/makefile - lines changed 12, context: html, text, full: html, text
- src/cdnaAli/exonAli/makefile - lines changed 15, context: html, text, full: html, text
- src/cdnaAli/findCdna/makefile - lines changed 11, context: html, text, full: html, text
- src/cdnaAli/g2cCheck/makefile - lines changed 16, context: html, text, full: html, text
- src/cdnaAli/introns/makefile - lines changed 12, context: html, text, full: html, text
- src/cdnaAli/pairClo/makefile - lines changed 10, context: html, text, full: html, text
- src/cdnaAli/patCount/makefile - lines changed 9, context: html, text, full: html, text
- src/cdnaAli/patSpace/makefile - lines changed 10, context: html, text, full: html, text
- src/cdnaAli/refineAli/makefile - lines changed 10, context: html, text, full: html, text
- src/cdnaAli/sortFilt/makefile - lines changed 10, context: html, text, full: html, text
- src/cdnaAli/stitchea/makefile - lines changed 10, context: html, text, full: html, text
- using new minimal makefile construction refs #9104
- src/index/bptForTwoBit/makefile - lines changed 14, context: html, text, full: html, text
- src/index/bptLookupStringToBits64/makefile - lines changed 14, context: html, text, full: html, text
- src/index/bptMakeStringToBits64/makefile - lines changed 14, context: html, text, full: html, text
- src/index/fofFa/makefile - lines changed 10, context: html, text, full: html, text
- src/index/indexRa/makefile - lines changed 11, context: html, text, full: html, text
- src/index/indexfa/makefile - lines changed 14, context: html, text, full: html, text
- src/index/indexgl/makefile - lines changed 15, context: html, text, full: html, text
- src/index/ixIxx/makefile - lines changed 14, context: html, text, full: html, text
- src/index/ixali/makefile - lines changed 11, context: html, text, full: html, text
- src/index/ixword1/makefile - lines changed 11, context: html, text, full: html, text
- src/index/ixword3/makefile - lines changed 11, context: html, text, full: html, text
- src/index/ixxenost/makefile - lines changed 11, context: html, text, full: html, text
- src/index/makepgo/makefile - lines changed 14, context: html, text, full: html, text
- src/index/stToXao/makefile - lines changed 11, context: html, text, full: html, text
- src/index/trixSearch/makefile - lines changed 14, context: html, text, full: html, text
- using new minimal makefile refs #9104
- src/hg/featureBits/makefile - lines changed 18, context: html, text, full: html, text
- eliminate the kludgy flag JKHGAPP from src/hg/ makefiles, can detect that in src/inc/userApp.mk, refs #9104
- src/hg/featureBits/makefile - lines changed 2, context: html, text, full: html, text
- src/hg/utils/gapToLift/makefile - lines changed 2, context: html, text, full: html, text
- using minimal makefile to allow build in kentUtils refs #9104
- src/hg/utils/oligoMatch/makefile - lines changed 14, context: html, text, full: html, text
- using new style minimal makefile for ordinary programs, not fixing CGI rules yet, removing obsolete CVS business, refs #9104
- src/utils/newProg/makefile - lines changed 10, context: html, text, full: html, text
- src/utils/newProg/newProg.c - lines changed 48, context: html, text, full: html, text
- minimal makefiles for kentUtils build refs #9104
- src/reformat/fatont4/makefile - lines changed 11, context: html, text, full: html, text
- src/reformat/gb2cdi/makefile - lines changed 12, context: html, text, full: html, text
- src/reformat/gbtofa/makefile - lines changed 10, context: html, text, full: html, text
- src/reformat/geniegff/makefile - lines changed 10, context: html, text, full: html, text
- src/reformat/gffgenes/makefile - lines changed 12, context: html, text, full: html, text
- src/reformat/moresyn/makefile - lines changed 11, context: html, text, full: html, text
- src/reformat/wabToSt/makefile - lines changed 13, context: html, text, full: html, text
- minimal makefiles for kentUtils build refs #9104
- src/xenoAli/bwana/makefile - lines changed 11, context: html, text, full: html, text
- src/xenoAli/dynAlign/makefile - lines changed 21, context: html, text, full: html, text
- src/xenoAli/stitcher/makefile - lines changed 11, context: html, text, full: html, text
- correct relative reference to jkOwnLib refs #9104
- src/cdnaAli/aliGlue/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/exonAli/makefile - lines changed 1, context: html, text, full: html, text
- src/cdnaAli/refineAli/makefile - lines changed 1, context: html, text, full: html, text
- minimal makefile for kentUtils build refs #9104
- src/scanIntrons/makefile - lines changed 17, context: html, text, full: html, text
- src/weblet/bottleneck/makefile - lines changed 14, context: html, text, full: html, text
- src/weblet/counter/makefile - lines changed 17, context: html, text, full: html, text
- src/weblet/hitreport/makefile - lines changed 15, context: html, text, full: html, text
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