File Changes for hiram

v241_preview to v241_base (2010-09-21 to 2010-09-28) v241

• src/hg/htdocs/images/phylo/ce9_10way.png
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    10-way diagram for C. elegans ce9/WS210
• src/hg/inc/agpFrag.h
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    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/lib/agpFrag.c
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    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/makeDb/doc/bruMal1.txt
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    running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/caeJap3.txt
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    done with repeat simple and window masking with kluster scratch ready to copy
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    running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/caePb2.txt
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/calJac3.txt
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    fixup gold/gap tables with fixed hgGoldGapGl procedure
• src/hg/makeDb/doc/cb3.txt
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/ce9.txt
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    running lastz runs on ce9 for melHap1 melInc1 bruMal1 and caeJap3
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    done with 10 nematode pair wise alignments
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    initial run of the 10-way multiz done
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    added gap annotations
• src/hg/makeDb/doc/melHap1.txt
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    done with repeat simple and window masking with kluster scratch ready to copy
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/melInc1.txt
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    done with repeat simple and window masking with kluster scratch ready to copy
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/doc/priPac1.txt
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    done with 10 nematode pair wise alignments
• src/hg/makeDb/genbank/etc/genbank.conf
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    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/src/lib/gbGenome.c
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    adding haeCon melHap melInc and bruMal nematodes: Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita, Brugia malayi
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    melNap is melHap
• src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
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    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/makeDb/hgGoldGapGl/hgLoadGap.c
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    moved the single use of agpFragValidate into hgGoldGapGl and fixup recognition of actual chrom name length
• src/hg/makeDb/hgLoadBed/makefile
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    install files should remove the destination before cp -p
• src/hg/makeDb/trackDb/makefile
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    adding caeJap3 to the build
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    adding haeCon1 to the build
• src/hg/makeDb/trackDb/tagTypes.tab
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    initial 10-way alignment on C. elegans/ce9/WS210
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    done with 10 nematode pair wise alignments
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    initial 10-way alignment on C. elegans/ce9/WS210
• src/hg/makeDb/trackDb/worm/caeJap3/description.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeJap3/gap.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeJap3/gold.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/caeJap3/trackDb.ra
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
  • lines changed 151, context: html, text, full: html, text
    initial 10-way alignment on C. elegans/ce9/WS210
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    added gap annotations
• src/hg/makeDb/trackDb/worm/haeCon1/description.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/haeCon1/gap.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/haeCon1/gold.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/haeCon1/trackDb.ra
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/worm/trackDb.ra
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    done with 10 nematode pair wise alignments
• src/hg/utils/automation/makeGenomeDb.pl
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    turn the quality track into a bigWig instead of wiggle
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    use featureBits to verify gold and gap tables cover all bases
• src/hg/utils/phyloTrees/nematodes.txt
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    ten nematodes from NCBI taxonomy
• src/inc/cgi_build_rules.mk
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    install files should remove the destination before cp -p
• src/product/scripts/trashCleaner.csh
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    need to output a status message when all files are done