Commits on Jan 31, 2014
  1. @joelarmstrong

    working better

    joelarmstrong committed Jan 31, 2014
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    working?

    joelarmstrong committed Jan 31, 2014
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Commits on Jan 30, 2014
  1. @ngannguyen
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Commits on Jan 28, 2014
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    Change up halContiguousRegions to work w/ preserving structure def

    Should still work with old "contiguous" definition with the right
    options.
    joelarmstrong committed Jan 28, 2014
Commits on Jan 25, 2014
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Commits on Jan 24, 2014
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Commits on Jan 22, 2014
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    Fix halGenomeTest failing

    joelarmstrong committed Jan 22, 2014
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    Merge branch 'modificationTools' of https://github.com/glennhickey/hal

    …into development
    
    Conflicts:
    	Makefile
    	stats/impl/halStatsMain.cpp
    
    Tests fail--but they didn't work in the first place.
    joelarmstrong committed Jan 21, 2014
Commits on Jan 21, 2014
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Commits on Jan 19, 2014
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    Remove debug print

    joelarmstrong committed Jan 18, 2014
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    Revert "Fix PSL output when lifting to negative strand on target"

    This reverts commit 06f8323.
    
    Wasn't clear on the difference between "+-" and "-" strands in PSL
    format.
    joelarmstrong committed Jan 18, 2014
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    Add option to print potential sites to halIndels

    Still untested--and there is a lot of waste in computing them. It
    doesn't compute bad columns twice, but it does compute good columns
    more than once when it doesn't need to.
    joelarmstrong committed Jan 18, 2014
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Commits on Jan 18, 2014
  1. revise last change to allow more flexibility to halBlockViz interface…

    … wrt returning dna sequence
    Glenn Hickey committed Jan 18, 2014
  2. fix bug where not using --outHalDir option caused problems for some i…

    …nput paths
    Glenn Hickey committed Jan 18, 2014
  3. change browser api to only return sequence data for lod 0, overriding…

    … the getSEquence parameter if necessary
    Glenn Hickey committed Jan 18, 2014
  4. Revert "fix compile error related to function pointer types"

    This reverts commit 9ccccfb.
    committed Jan 18, 2014
  5. fix compile error related to function pointer types

    Glenn Hickey committed Jan 18, 2014
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Commits on Jan 17, 2014
  1. @joelarmstrong
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    Clean up halIndels output

    joelarmstrong committed Jan 16, 2014
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