Commits · ac0c3909803cf389efc12d729bd084f3df48c47b · violethaze74 / Artemis

Apr 14, 2011

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15956 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ac0c3909

remove print · ab5923e6

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15953 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ab5923e6

changes to filtering of reads · 586bcf51

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15952 ee4ac58c-ac51-4696-9907-e4b3aa274f04

586bcf51

load BAM/VCF using SwingWorker · 81bac1eb

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15951 ee4ac58c-ac51-4696-9907-e4b3aa274f04

81bac1eb

Apr 13, 2011

filter duplicates · bf965aa7

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15943 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bf965aa7

join predicates together · 6bb314b8

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15942 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6bb314b8

set visibility of flags to protected · 868930cf

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15941 ee4ac58c-ac51-4696-9907-e4b3aa274f04

868930cf

Apr 08, 2011

report number of mapped reads · 91f04cef

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15897 ee4ac58c-ac51-4696-9907-e4b3aa274f04

91f04cef

add option to rpkm calculation · f047f7b4

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15896 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f047f7b4

VCF insertion colour is magenta · 9d661f5c

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15890 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9d661f5c

Apr 07, 2011

update · bee691c2

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15880 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bee691c2

add option to create features from variants · f3c67303

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15879 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f3c67303

Apr 06, 2011

change to FileViewer · 1aa07fb6

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15876 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1aa07fb6

change to FileViewer to save · ef15fef7

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15874 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ef15fef7

change to FileViewer · d82ab464

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15873 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d82ab464

change to FileViewer · a2941587

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15872 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a2941587

change to FileViewer · ed708748

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15870 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ed708748

add option to write to file · 82b46216

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15869 ee4ac58c-ac51-4696-9907-e4b3aa274f04

82b46216

Apr 05, 2011

add option to count reads for selected features · f6420b58

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15867 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f6420b58

Mar 31, 2011

add options to command line · a0b64dd5

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15859 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a0b64dd5

update · 2ff13cd7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15858 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2ff13cd7

fixes for BAM and VCF views · f6cb9131

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15857 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f6cb9131

add getVcfView() · 6e171858

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15856 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6e171858

Mar 30, 2011

use cache to avoid drawing over a variant with a non-variant · 97cfaa9b

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15848 ee4ac58c-ac51-4696-9907-e4b3aa274f04

97cfaa9b

fix for saving prompt configuration · 08259703

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15847 ee4ac58c-ac51-4696-9907-e4b3aa274f04

08259703

use N for filtered sites · 6fe78b6d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15844 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6fe78b6d

Mar 29, 2011

warn if trying to write out indexed fasta · 1eed7915

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15842 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1eed7915

use N's for SNPs and non-variant sites not passing filter · db7627b7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15841 ee4ac58c-ac51-4696-9907-e4b3aa274f04

db7627b7

speed up non-variant display · fc664233

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15840 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fc664233

make reference uppercase · b3071090

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15839 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b3071090

fixes for making reference uppercase · d8e7dce6

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15838 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d8e7dce6

make non-variant translucent · d8c8bbc9

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15836 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d8c8bbc9

tidy · 51ec7f7b

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15835 ee4ac58c-ac51-4696-9907-e4b3aa274f04

51ec7f7b

cache info parts in getInfoValue() · ada38430

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15834 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ada38430

optimise isMultiAllele() · fa5a0054

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15832 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fa5a0054

use pattern to speed up getFormatValue() · b88c2f67

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15831 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b88c2f67

Mar 28, 2011

fix for insertions/deletion in VCF v3 · 9adb63fb

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15828 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9adb63fb

fix for headers - removal of space · 9329e0b2

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15827 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9329e0b2

non-variants are light grey and insertions are magenta · d87b4c18

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15826 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d87b4c18

AF1 filtered - except for non-variant sites · 34a2759f

tjc authored 14 years ago

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

34a2759f

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