Commits for galt

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

• 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/hgTables/gffOut.c - lines changed 19, 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/hg/lib/trackHub.c - lines changed 5, context: html, text, full: html, text
  • src/inc/htmlPage.h - lines changed 5, context: html, text, full: html, text
  • src/lib/htmlPage.c - lines changed 52, context: html, text, full: html, text
• Merging in bigWigCat shared branch with --squash. This is Daniel Zerbino's work.
  • src/inc/bigWig.h - lines changed 2, context: html, text, full: html, text
  • src/inc/bwgInternal.h - lines changed 2, context: html, text, full: html, text
  • src/inc/cirTree.h - lines changed 3, context: html, text, full: html, text
  • src/lib/bwgCreate.c - lines changed 179, context: html, text, full: html, text
  • src/lib/cirTree.c - lines changed 95, context: html, text, full: html, text
  • src/utils/bigWigCat/bigWigCat.c - lines changed 630, context: html, text, full: html, text
  • src/utils/bigWigCat/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tbg1.sum - lines changed 1, context: html, text, full: html, text
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  • src/utils/bigWigCat/tests/expected/testBedGraph.bedGraph - lines changed 64, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/testFixed.bedGraph - lines changed 82, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/testVar.bedGraph - lines changed 72, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tf1.sum - lines changed 1, context: html, text, full: html, text
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  • src/utils/bigWigCat/tests/input/test.sizes - lines changed 49, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/input/testBedGraph_A.wig - lines changed 42, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/input/testBedGraph_B.wig - lines changed 22, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/input/testFixed_A.wig - lines changed 50, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/input/testFixed_B.wig - lines changed 56, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/input/testVar_A.wig - lines changed 51, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/input/testVar_B.wig - lines changed 26, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/makefile - lines changed 60, context: html, text, full: html, text
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/expected/testBedGraph.bedGraph - lines changed 64, context: html, text, full: html, text
  • src/utils/wigToBigWig/expected/testFixed.bedGraph - lines changed 100, context: html, text, full: html, text
  • src/utils/wigToBigWig/expected/testVar.bedGraph - lines changed 72, context: html, text, full: html, text
  • src/utils/wigToBigWig/expected/tf1.sum - lines changed 1, context: html, text, full: html, text
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  • src/utils/wigToBigWig/expected/tv1.sum - lines changed 1, context: html, text, full: html, text
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  • src/utils/wigToBigWig/test.sh - lines changed 50, context: html, text, full: html, text
  • src/utils/wigToBigWig/test.sizes - lines changed 49, context: html, text, full: html, text
  • src/utils/wigToBigWig/testBedGraph.wig - lines changed 64, context: html, text, full: html, text
  • src/utils/wigToBigWig/testFixed.wig - lines changed 106, context: html, text, full: html, text
  • src/utils/wigToBigWig/testVar.wig - lines changed 77, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected/tbg1.sum - lines changed 1, context: html, text, full: html, text
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  • src/utils/wigToBigWig/tests/input/test.sizes - lines changed 49, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/input/testBedGraph.wig - lines changed 64, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/input/testFixed.wig - lines changed 106, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/input/testVar.wig - lines changed 77, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/makefile - lines changed 98, context: html, text, full: html, text
  • src/utils/wigToBigWig/wigToBigWig.c - lines changed 10, context: html, text, full: html, text