Commits · bf90c8fd882b3afd7c0877363f0332d2c0f821a0 · violethaze74 / Artemis

Feb 22, 2011

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

dialog to show files that have been written to · c22d41c9

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15563 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c22d41c9

organise menu for writing and viewing fasta · 48e09f7d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15562 ee4ac58c-ac51-4696-9907-e4b3aa274f04

48e09f7d

further checks and fixes to exportFasta · 335d7574

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15561 ee4ac58c-ac51-4696-9907-e4b3aa274f04

335d7574

add more IUB codes · 4927ed51

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15560 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4927ed51

add getName() · 3d9efd1c

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15559 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3d9efd1c

Feb 17, 2011

handle heterozygous sites · 68122d3d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15556 ee4ac58c-ac51-4696-9907-e4b3aa274f04

68122d3d

add option to view VCF sequence · 2f5ec5b2

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15555 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2f5ec5b2

more fixes for identifying heterozygous sites · d3024a80

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15553 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d3024a80

fixes to getSeqsVariation() · f63be8a9

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15552 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f63be8a9

fix in getNumberOfDeletions() · 4441ba86

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15551 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4441ba86

tidy and make non-variant lines shorter · 9622857f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15550 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9622857f

Feb 16, 2011

fix for isNonVariant() · 0567a0ef

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15545 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0567a0ef

use genotype phred likelihood to determine if heterozygous · 6e75a6a2

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15535 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6e75a6a2

Feb 15, 2011

changes to getSeqsVariation() · d5778f28

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15521 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d5778f28

Add VCFRecord.VariantBase class and more on export of fasta · 1a830602

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15520 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1a830602

Feb 14, 2011

introduce a BCFReaderIterator and fix for BCFReader.getPart() · 05f49916

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15507 ee4ac58c-ac51-4696-9907-e4b3aa274f04

05f49916

Feb 10, 2011

add option to show non-variants and provide file selection when exporting · c3fd9c03

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15486 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c3fd9c03

remove unused import · 6e6ac81d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15483 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6e6ac81d

Feb 01, 2011

use DatabaseTreeNode.setOrganismProps for db entriess · f79b2d1b

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15409 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f79b2d1b

use DatabaseTreeNode.setOrganismProps · 4a9646c0

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15408 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4a9646c0

tidy · 3682f080

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15407 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3682f080

add setOrganismProps · b1ee4c59

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15406 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b1ee4c59

use property (artemis.user.dir.prompt) to show or hide user dir prompt at start of session · b73704e9
tjc authored 14 years ago
```
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15405 ee4ac58c-ac51-4696-9907-e4b3aa274f04
```
b73704e9

use organismprop to set if read only · 54f25a42

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15404 ee4ac58c-ac51-4696-9907-e4b3aa274f04

54f25a42

update · 94102cec

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15403 ee4ac58c-ac51-4696-9907-e4b3aa274f04

94102cec

Jan 26, 2011

fix for reading fasta with java less than 1.6 · 18cf107f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15370 ee4ac58c-ac51-4696-9907-e4b3aa274f04

18cf107f

Jan 13, 2011

add picard to CLASSPATH · a0d1e828

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15327 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a0d1e828

catch number format exception for quality · d822e697

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15326 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d822e697

Jan 12, 2011

add fasta extensions · b0c10b41

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15325 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b0c10b41

Admin message

Admin message