File Changes for galt

v293_base to v294_preview (2013-12-09 to 2013-12-16) v294

• src/hg/hgTables/gffOut.c
  • lines changed 19, context: html, text, full: html, text
    fixes 12318. for assemblies like rheMac3 that have many thousands of chroms, it is faster to find out a distinct list of chroms that are actually used by the e.g. refGene table and hash them, and then can quickly skip thousands of regions not in the hash. now it goes from timing out over 3 minutes to returning a good result in a few seconds.
• src/hg/lib/trackHub.c
  • lines changed 5, context: html, text, full: html, text
    fixes #12337. better way to allow colons in urls by splitting htmlExpandUrl into two functions. the new one is called expandUrlOnBase and includes ftp support as well as http(s).
• src/inc/bigWig.h
  • lines changed 2, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/inc/bwgInternal.h
  • lines changed 2, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/inc/cirTree.h
  • lines changed 3, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/inc/htmlPage.h
  • lines changed 5, context: html, text, full: html, text
    fixes #12337. better way to allow colons in urls by splitting htmlExpandUrl into two functions. the new one is called expandUrlOnBase and includes ftp support as well as http(s).
• src/lib/bwgCreate.c
  • lines changed 179, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/lib/cirTree.c
  • lines changed 95, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/lib/htmlPage.c
  • lines changed 52, context: html, text, full: html, text
    fixes #12337. better way to allow colons in urls by splitting htmlExpandUrl into two functions. the new one is called expandUrlOnBase and includes ftp support as well as http(s).
• src/utils/bigWigCat/bigWigCat.c
  • lines changed 630, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/makefile
  • lines changed 3, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tbg1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tbg10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tbg100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tbg1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tbg10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/testBedGraph.bedGraph
  • lines changed 64, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/testFixed.bedGraph
  • lines changed 82, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/testVar.bedGraph
  • lines changed 72, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf3.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf30.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf300.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tf3000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tv1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tv10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tv100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tv1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/expected/tv10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/test.sizes
  • lines changed 49, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/testBedGraph_A.wig
  • lines changed 42, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/testBedGraph_B.wig
  • lines changed 22, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/testFixed_A.wig
  • lines changed 50, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/testFixed_B.wig
  • lines changed 56, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/testVar_A.wig
  • lines changed 51, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/input/testVar_B.wig
  • lines changed 26, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/bigWigCat/tests/makefile
  • lines changed 60, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/testBedGraph.bedGraph
  • lines changed 64, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/testFixed.bedGraph
  • lines changed 100, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/testVar.bedGraph
  • lines changed 72, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf3.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf30.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf300.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tf3000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tv1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tv10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tv100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tv1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/expected/tv10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/test.sh
  • lines changed 50, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/test.sizes
  • lines changed 49, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/testBedGraph.wig
  • lines changed 64, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/testFixed.wig
  • lines changed 106, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/testVar.wig
  • lines changed 77, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tbg1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tbg10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tbg100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tbg1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tbg10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/testBedGraph.bedGraph
  • lines changed 64, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/testFixed.bedGraph
  • lines changed 82, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/testVar.bedGraph
  • lines changed 72, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf1.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf10.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf100.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf1000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf10000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf3.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf30.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf300.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tf3000.sum
  • lines changed 1, context: html, text, full: html, text
    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tv1.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tv10.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tv100.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tv1000.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected/tv10000.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/tbg1.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/tbg10.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/tbg100.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/tbg1000.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/tbg10000.sum
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/testBedGraph.bedGraph
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/testFixed.bedGraph
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/expected_2/testVar.bedGraph
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• src/utils/wigToBigWig/tests/expected_2/tf1.sum
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• src/utils/wigToBigWig/tests/expected_2/tf10.sum
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• src/utils/wigToBigWig/tests/expected_2/tf100.sum
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• src/utils/wigToBigWig/tests/expected_2/tf1000.sum
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• src/utils/wigToBigWig/tests/expected_2/tf10000.sum
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• src/utils/wigToBigWig/tests/expected_2/tf3.sum
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• src/utils/wigToBigWig/tests/expected_2/tf30.sum
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• src/utils/wigToBigWig/tests/expected_2/tf300.sum
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• src/utils/wigToBigWig/tests/expected_2/tf3000.sum
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• src/utils/wigToBigWig/tests/expected_2/tv1.sum
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• src/utils/wigToBigWig/tests/expected_2/tv10.sum
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• src/utils/wigToBigWig/tests/expected_2/tv100.sum
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• src/utils/wigToBigWig/tests/expected_2/tv1000.sum
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• src/utils/wigToBigWig/tests/expected_2/tv10000.sum
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• src/utils/wigToBigWig/tests/input/test.sizes
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/input/testBedGraph.wig
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• src/utils/wigToBigWig/tests/input/testFixed.wig
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    Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
• src/utils/wigToBigWig/tests/input/testVar.wig
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• src/utils/wigToBigWig/tests/makefile
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• src/utils/wigToBigWig/wigToBigWig.c
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