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Commits on Apr 11, 2011
Commits on Apr 8, 2011
  1. report number of mapped reads

    tjc committed Apr 8, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15897 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. add option to rpkm calculation

    tjc committed Apr 8, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15896 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  3. VCF insertion colour is magenta

    tjc committed Apr 8, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15890 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Apr 7, 2011
  1. update

    tjc committed Apr 7, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15880 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. add option to create features from variants

    tjc committed Apr 7, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15879 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Apr 6, 2011
  1. change to FileViewer

    tjc committed Apr 6, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15876 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. change to FileViewer to save

    tjc committed Apr 6, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15874 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  3. change to FileViewer

    tjc committed Apr 6, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15873 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  4. change to FileViewer

    tjc committed Apr 6, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15872 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  5. change to FileViewer

    tjc committed Apr 6, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15870 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  6. add option to write to file

    tjc committed Apr 6, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15869 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Apr 5, 2011
  1. add option to count reads for selected features

    tjc committed Apr 5, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15867 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Mar 31, 2011
  1. add options to command line

    tjc committed Mar 31, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15859 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. update

    tjc committed Mar 31, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15858 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  3. fixes for BAM and VCF views

    tjc committed Mar 31, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15857 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  4. add getVcfView()

    tjc committed Mar 31, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15856 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Mar 30, 2011
  1. use cache to avoid drawing over a variant with a non-variant

    tjc committed Mar 30, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15848 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. fix for saving prompt configuration

    tjc committed Mar 30, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15847 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  3. use N for filtered sites

    tjc committed Mar 30, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15844 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Mar 29, 2011
  1. warn if trying to write out indexed fasta

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15842 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. use N's for SNPs and non-variant sites not passing filter

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15841 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  3. speed up non-variant display

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15840 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  4. make reference uppercase

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15839 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  5. fixes for making reference uppercase

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15838 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  6. make non-variant translucent

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15836 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  7. tidy

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15835 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  8. cache info parts in getInfoValue()

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15834 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  9. optimise isMultiAllele()

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15832 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  10. use pattern to speed up getFormatValue()

    tjc committed Mar 29, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15831 ee4ac58c-ac51-4696-9907-e4b3aa274f04
Commits on Mar 28, 2011
  1. fix for insertions/deletion in VCF v3

    tjc committed Mar 28, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15828 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  2. fix for headers - removal of space

    tjc committed Mar 28, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15827 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  3. non-variants are light grey and insertions are magenta

    tjc committed Mar 28, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15826 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  4. AF1 filtered - except for non-variant sites

    tjc committed Mar 28, 2011
    git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15825 ee4ac58c-ac51-4696-9907-e4b3aa274f04