Commits · 5aee7aff0ddcb9b9d5df303ed57716afc465c4af · violethaze74 / Artemis

Jul 26, 2011
- fix to run in headless · 5aee7aff
  tcarver authored 13 years ago
  
  5aee7aff
- change to TransferAnnotationTool constructor · ccacc935
  tcarver authored 13 years ago
  
  ccacc935
- add button to import cluster names · 26ed756c
  tcarver authored 13 years ago
  
  26ed756c
- add getGeneNameList(boolean cluster) method · 3b42c125
  tcarver authored 13 years ago
  
  3b42c125
Jul 19, 2011
- changes so checkSyn can be used without artemis feature · 1e529583
  tcarver authored 13 years ago
  
  1e529583
- if UTR belongs to single transcript gene use gene id as the locus_tag · 2e9623fe
  tcarver authored 13 years ago
  
  2e9623fe
- update · 84fcbbea
  tcarver authored 13 years ago
  
  84fcbbea
Jul 13, 2011
- update readme · 1dc4af5a
  tcarver authored 13 years ago
  
  1dc4af5a
Jul 06, 2011

add mappings for snRNA and snoRNA · 12977490

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16395 ee4ac58c-ac51-4696-9907-e4b3aa274f04

12977490

Jun 27, 2011

fix for reading BCF files · 382bfbd1

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16353 ee4ac58c-ac51-4696-9907-e4b3aa274f04

382bfbd1

addiotonal docs for analyses etc · cbbfe050

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16352 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cbbfe050

addiotonal docs for analyses etc · 29f696a4

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16351 ee4ac58c-ac51-4696-9907-e4b3aa274f04

29f696a4

addiotonal docs for analyses etc · 112f0326

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16350 ee4ac58c-ac51-4696-9907-e4b3aa274f04

112f0326

fix for userplot typo · eaf56e9d

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16348 ee4ac58c-ac51-4696-9907-e4b3aa274f04

eaf56e9d

update · 2dff6d6c

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16347 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2dff6d6c

Jun 24, 2011

'Use N for filtered out sites' option set to true by default · 93612b57

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16337 ee4ac58c-ac51-4696-9907-e4b3aa274f04

93612b57

Jun 22, 2011

ignore non-variants when using synonymous/non-synonymous colour scheme · 0ad0b265

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16311 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0ad0b265

Jun 15, 2011

update · cacdf4ab

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16290 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cacdf4ab

optionally include mapped reads to all reference sequences in RPKM calculation · 73b39082

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16289 ee4ac58c-ac51-4696-9907-e4b3aa274f04

73b39082

Jun 07, 2011

auto-completion for reference sequence selection · a28d2329

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16230 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a28d2329

Jun 06, 2011

constructor with Vectors of unknown type · bda785ca

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16223 ee4ac58c-ac51-4696-9907-e4b3aa274f04

bda785ca

use JComboBox in constructor · 1645e466

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16222 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1645e466

add option to hide individual VCF files · ad0a8aa2

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16218 ee4ac58c-ac51-4696-9907-e4b3aa274f04

ad0a8aa2

Jun 02, 2011

catch ArrayIndexOutOfBoundsException thrown by tabix when reference is not found · 2dfde6a8

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16203 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2dfde6a8

Jun 01, 2011

add modified_amino_acid_feature · a27f0639

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16194 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a27f0639

update · d515f00d

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16193 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d515f00d

May 31, 2011

BamView checks the sequence length matches the BAM header (SQ) length · 319794b7

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16186 ee4ac58c-ac51-4696-9907-e4b3aa274f04

319794b7

May 17, 2011

correction · 47c45740

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16156 ee4ac58c-ac51-4696-9907-e4b3aa274f04

47c45740

May 16, 2011

update · 64a46415

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16155 ee4ac58c-ac51-4696-9907-e4b3aa274f04

64a46415

update · 8c1eeb69

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16154 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8c1eeb69

remove synchronized on the read routines · 3c292c4f

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16153 ee4ac58c-ac51-4696-9907-e4b3aa274f04

3c292c4f

May 13, 2011

add commons-net · 77121494

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16136 ee4ac58c-ac51-4696-9907-e4b3aa274f04

77121494

add FTPSeekableStream logger · cc8cea17

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16135 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cc8cea17

add commons-net · e29d7684

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16133 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e29d7684

add commons-net · d138cd53

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16132 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d138cd53

use FTPSeekableStream to support BAM files over FTP · 1f3cb4cf

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16129 ee4ac58c-ac51-4696-9907-e4b3aa274f04

1f3cb4cf

additional constructors to handle files over http and ftp · a8b1dea9

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16128 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a8b1dea9

changes to use FTPSeekableStream to support files over FTP · f3579a17

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16127 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f3579a17

isBCF() handles files over FTP · 7d4189cd

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16126 ee4ac58c-ac51-4696-9907-e4b3aa274f04

7d4189cd

use FTPSeekableStream to support files over FTP · 72d8a557

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16124 ee4ac58c-ac51-4696-9907-e4b3aa274f04

72d8a557

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