Commits · e500d6dd705f8e8259d970df0a62744e9302e627 · violethaze74 / Artemis

Mar 07, 2011

calculate SNP plot when reading in BAM · e500d6dd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15673 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e500d6dd

move drawMax() · 79cda9e3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15672 ee4ac58c-ac51-4696-9907-e4b3aa274f04

79cda9e3

move drawMax() to AbstractGraphPanel · 495890d1

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15671 ee4ac58c-ac51-4696-9907-e4b3aa274f04

495890d1

draw the read coverage and scale if needed · 8285a7b0

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15663 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8285a7b0

reset redraw variable · de08cb0e

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15662 ee4ac58c-ac51-4696-9907-e4b3aa274f04

de08cb0e

Mar 02, 2011

set menu fonts · cfbbfb87

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15640 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cfbbfb87

change zoom out so it switches to a coverage plot · 577afa99

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15638 ee4ac58c-ac51-4696-9907-e4b3aa274f04

577afa99

Mar 01, 2011

fix for finding synonymous and non-synonymous variants · 5c5a11da

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15629 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5c5a11da

Feb 28, 2011

fix for cancel write to file · 1bb3c28e

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15621 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1bb3c28e

add options for saving FASTA files · cb3bd1a9

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15620 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cb3bd1a9

Feb 25, 2011

update · 4356f355

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15619 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4356f355

add option to show / hide labels · 92050038

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15618 ee4ac58c-ac51-4696-9907-e4b3aa274f04

92050038

add option to write to single or multiple files · f51d12b2

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15617 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f51d12b2

Feb 24, 2011

update · 6928ddd9

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15611 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6928ddd9

tidy · 1a4ca9aa

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15610 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1a4ca9aa

add graphs · c99b1b9d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15609 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c99b1b9d

use vcf_v4 recorded in AbstractVCFReader and tidy · 768b5c5a

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15606 ee4ac58c-ac51-4696-9907-e4b3aa274f04

768b5c5a

tidy and changes for concatenation case · 91b0cf71

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15605 ee4ac58c-ac51-4696-9907-e4b3aa274f04

91b0cf71

change MULTI_ALLELE_PATTERN to look for lowercase bases · 7ddd640e

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15604 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7ddd640e

record version number · 10c040fe

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15603 ee4ac58c-ac51-4696-9907-e4b3aa274f04

10c040fe

Feb 23, 2011

add menu separator · 26754ec3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15602 ee4ac58c-ac51-4696-9907-e4b3aa274f04

26754ec3

fix filter suffix · 07e175d6

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15601 ee4ac58c-ac51-4696-9907-e4b3aa274f04

07e175d6

update · 9b5a1989

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15599 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9b5a1989

update · f8bcb218

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15598 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f8bcb218

remove jars chado and retrotranslator · 077e3fb8

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15597 ee4ac58c-ac51-4696-9907-e4b3aa274f04

077e3fb8

update · 1ea78bcf

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15596 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1ea78bcf

remove chado java 1.4 pojo's · 0c7e27e3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15595 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0c7e27e3

Feb 22, 2011

wrap sequence string · f8b26651

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15584 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f8b26651

update · e5408ada

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15583 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e5408ada

fix for getSequenceOffset() · bf90c8fd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15582 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bf90c8fd

optimise split() functions · d348a2ca

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15581 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d348a2ca

optimise passFilter() · 99954024

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15580 ee4ac58c-ac51-4696-9907-e4b3aa274f04

99954024

implement getBasesInRegion() · fdcd4842

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15579 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fdcd4842

optimise getParts() · c3fff51b

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15578 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c3fff51b

Feb 21, 2011

implementation for VCF · 2b194143

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15573 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2b194143

update · b6b7aec3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15572 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b6b7aec3

use getNumberofIndels() · 426f0590

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15571 ee4ac58c-ac51-4696-9907-e4b3aa274f04

426f0590

warn if nothing is selected · 159b5d18

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15570 ee4ac58c-ac51-4696-9907-e4b3aa274f04

159b5d18

open file viewer with multiple fasta · e38b967d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15569 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e38b967d

Feb 18, 2011

changes for writing out fasta of base ranges · 1eb3283f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15564 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1eb3283f

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