Commits for hiram
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v241_preview to v241_base (2010-09-21 to 2010-09-28) v241
- turn the quality track into a bigWig instead of wiggle
- src/hg/utils/automation/makeGenomeDb.pl - lines changed 9, context: html, text, full: html, text
- initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeJap3/description.html - lines changed 129, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/caeJap3/gap.html - lines changed 64, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/caeJap3/gold.html - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/caeJap3/trackDb.ra - lines changed 40, context: html, text, full: html, text
- adding caeJap3 to the build
- src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
- done with repeat simple and window masking with kluster scratch ready to copy
- src/hg/makeDb/doc/melHap1.txt - lines changed 87, context: html, text, full: html, text
- done with repeat simple and window masking with kluster scratch ready to copy
- src/hg/makeDb/doc/melInc1.txt - lines changed 81, context: html, text, full: html, text
- done with repeat simple and window masking with kluster scratch ready to copy
- src/hg/makeDb/doc/caeJap3.txt - lines changed 120, context: html, text, full: html, text
- need to output a status message when all files are done
- src/product/scripts/trashCleaner.csh - lines changed 12, context: html, text, full: html, text
- moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
- src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c - lines changed 48, context: html, text, full: html, text
- src/hg/makeDb/hgGoldGapGl/hgLoadGap.c - lines changed 21, context: html, text, full: html, text
- fixup gold/gap tables with fixed hgGoldGapGl procedure
- src/hg/makeDb/doc/calJac3.txt - lines changed 25, context: html, text, full: html, text
- running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
- src/hg/makeDb/doc/bruMal1.txt - lines changed 103, context: html, text, full: html, text
- src/hg/makeDb/doc/caeJap3.txt - lines changed 44, context: html, text, full: html, text
- src/hg/makeDb/doc/ce9.txt - lines changed 416, context: html, text, full: html, text
- install files should remove the destination before cp -p
- src/hg/makeDb/hgLoadBed/makefile - lines changed 21, context: html, text, full: html, text
- src/inc/cgi_build_rules.mk - lines changed 3, context: html, text, full: html, text
- use featureBits to verify gold and gap tables cover all bases
- src/hg/utils/automation/makeGenomeDb.pl - lines changed 12, context: html, text, full: html, text
- initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/haeCon1/description.html - lines changed 129, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/haeCon1/gap.html - lines changed 64, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/haeCon1/gold.html - lines changed 23, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/haeCon1/trackDb.ra - lines changed 40, context: html, text, full: html, text
- adding haeCon1 to the build
- src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
- done with 10 nematode pair wise alignments
- src/hg/makeDb/doc/bruMal1.txt - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/doc/caeJap3.txt - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/doc/caePb2.txt - lines changed 25, context: html, text, full: html, text
- src/hg/makeDb/doc/cb3.txt - lines changed 24, context: html, text, full: html, text
- src/hg/makeDb/doc/ce9.txt - lines changed 182, context: html, text, full: html, text
- src/hg/makeDb/doc/melHap1.txt - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/doc/melInc1.txt - lines changed 19, context: html, text, full: html, text
- src/hg/makeDb/doc/priPac1.txt - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 504, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/trackDb.ra - lines changed 158, context: html, text, full: html, text
- ten nematodes from NCBI taxonomy
- src/hg/utils/phyloTrees/nematodes.txt - lines changed 25, context: html, text, full: html, text
- 10-way diagram for C. elegans ce9/WS210
- src/hg/htdocs/images/phylo/ce9_10way.png - lines changed 0, context: html, text, full: html, text
- initial run of the 10-way multiz done
- src/hg/makeDb/doc/ce9.txt - lines changed 229, context: html, text, full: html, text
- initial 10-way alignment on C. elegans/ce9/WS210
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 113, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/ce9/trackDb.ra - lines changed 151, context: html, text, full: html, text
- added gap annotations
- src/hg/makeDb/doc/ce9.txt - lines changed 88, context: html, text, full: html, text
- src/hg/makeDb/trackDb/worm/ce9/trackDb.ra - lines changed 1, context: html, text, full: html, text
- adding caeJap3 C. japonica WUGSC 7.0.1, haeCon1 H. contortus WS210, melHap1 M. hapla WS210, melInc1 M. incognita WS210, bruMal1 B. malayi WS210
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 98, context: html, text, full: html, text
- adding haeCon melHap melInc and bruMal nematodes: Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita, Brugia malayi
- src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 8, context: html, text, full: html, text
- melNap is melHap
- src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text
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