Commits · 47c457401d0ef28abadcc6b2b2ea2e9a33d347f1 · violethaze74 / Artemis

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

apache commons-net · 5599de30

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16123 ee4ac58c-ac51-4696-9907-e4b3aa274f04

5599de30

FTPSeekableStream for BAM and BCF / VCF · 0a9da6c6

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16120 ee4ac58c-ac51-4696-9907-e4b3aa274f04

0a9da6c6

May 12, 2011

update · fcc26dad

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16076 ee4ac58c-ac51-4696-9907-e4b3aa274f04

fcc26dad

use filter when calculating overview · d54c272c

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16075 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d54c272c

allow for X · 42c891a1

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16073 ee4ac58c-ac51-4696-9907-e4b3aa274f04

42c891a1

allow for SP type change in bcftoools · e5471855

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16072 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e5471855

May 11, 2011

add TableViewer to display data in JTable · 2d9f0c0c

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16069 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2d9f0c0c

set cursor to busy when count variant types · 2aa247db

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16068 ee4ac58c-ac51-4696-9907-e4b3aa274f04

2aa247db

May 10, 2011

update version · a7392a77

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16067 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a7392a77

make class public · 6967f883

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16066 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6967f883

use AbstractVCFReader.getNextRecord() and add variation overview option · e55f2785

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16065 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e55f2785

Apr 27, 2011

fix for variants without a format · abf49527

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16002 ee4ac58c-ac51-4696-9907-e4b3aa274f04

abf49527

Apr 26, 2011
- changes for the "Create introns" function to transfer sys_id and allow for 3'UTR and 5'UTR · af7a78d9
  tjc authored 13 years ago
  
  git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15998 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  af7a78d9
Apr 21, 2011

update · d62b286f

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15992 ee4ac58c-ac51-4696-9907-e4b3aa274f04

d62b286f

use progress bar for read count calculation · 9bf4f570

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15991 ee4ac58c-ac51-4696-9907-e4b3aa274f04

9bf4f570

Apr 20, 2011

disable analyse menus when no FeatureDisplay · f0e143bf

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15983 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f0e143bf

Apr 18, 2011

update · de080ea0

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15968 ee4ac58c-ac51-4696-9907-e4b3aa274f04

de080ea0

Apr 15, 2011

update · e015248e

tjc authored 13 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15963 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e015248e

Apr 14, 2011

rpkm changes · ac0c3909

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

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