Commits · a13476fef0fc3cdeb4e10fb3c63f27e3a7be1343 · violethaze74 / Artemis

Mar 16, 2011

tests for writing out sequences based on VCF data · a13476fe

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15732 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a13476fe

change for artemis_options · c77d1613

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15731 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c77d1613

fix for insertion · e23f8c58

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15729 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e23f8c58

Mar 15, 2011

changes for test · dea77072

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15726 ee4ac58c-ac51-4696-9907-e4b3aa274f04

dea77072

fix for blast+ output · 4ff25f31

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15725 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4ff25f31

remove unused import · 468e6d06

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15724 ee4ac58c-ac51-4696-9907-e4b3aa274f04

468e6d06

fix for writing out VCF from HTTP · 8866d301

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15723 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8866d301

fix for reverse strand · b12080fb

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15722 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b12080fb

catch NullPointerException from TabixReader · 09c8d323

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15721 ee4ac58c-ac51-4696-9907-e4b3aa274f04

09c8d323

catch exceptions from TabixReader · 7ce1e92a

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15720 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7ce1e92a

optimise writing region · 559076e0

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15719 ee4ac58c-ac51-4696-9907-e4b3aa274f04

559076e0

update · 2157ea85

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15718 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2157ea85

add BCFReader · 04a715dd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15716 ee4ac58c-ac51-4696-9907-e4b3aa274f04

04a715dd

add logger · aaa57652

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15715 ee4ac58c-ac51-4696-9907-e4b3aa274f04

aaa57652

remove unused import · 89f16c23

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15714 ee4ac58c-ac51-4696-9907-e4b3aa274f04

89f16c23

Mar 14, 2011

chunk regions · 89273dee

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15713 ee4ac58c-ac51-4696-9907-e4b3aa274f04

89273dee

change visibility of iterator · 055ba5b2

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15712 ee4ac58c-ac51-4696-9907-e4b3aa274f04

055ba5b2

Mar 11, 2011

write/view reference sequence as well as vcf sequences · 5d4b8d09

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15704 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5d4b8d09

Mar 10, 2011

update · f8ece7b4

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15702 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f8ece7b4

tidy · 871d00be

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15701 ee4ac58c-ac51-4696-9907-e4b3aa274f04

871d00be

fix for changing window size in coverage plots · 10ff9298

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15700 ee4ac58c-ac51-4696-9907-e4b3aa274f04

10ff9298

add constructor and make border · 86e7dd82

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15699 ee4ac58c-ac51-4696-9907-e4b3aa274f04

86e7dd82

Mar 09, 2011

update · d4300777

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15689 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d4300777

space reads out more when orientation is displayed · 2e4218d4

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15688 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2e4218d4

Mar 08, 2011

tidy · 1720113f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15685 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1720113f

read remote BCF files · 1acd7b39

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15680 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1acd7b39

read remote BCF files · 7e4add4d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15678 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7e4add4d

Mar 07, 2011

update - add Coverage view to BamView · ec49e183

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15675 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ec49e183

update · 7d5a3fc1

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15674 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7d5a3fc1

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

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