Commits · ed7087480df5edbb7b0f99c5acf483146051c1f5 · violethaze74 / Artemis

Apr 05, 2011

add option to count reads for selected features · f6420b58

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15867 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f6420b58

Mar 31, 2011

add options to command line · a0b64dd5

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15859 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a0b64dd5

Mar 25, 2011

move clone window option · 213078c7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15817 ee4ac58c-ac51-4696-9907-e4b3aa274f04

213078c7

change border to dark grey · c1173ce0

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15816 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c1173ce0

Mar 24, 2011

add option to clone BamView panel · 6540bdbd

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15809 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6540bdbd

move code to BamView constructor · 387dc46b

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15807 ee4ac58c-ac51-4696-9907-e4b3aa274f04

387dc46b

ensure log option disabled for views other than inferred size · 66b161e8

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15803 ee4ac58c-ac51-4696-9907-e4b3aa274f04

66b161e8

Mar 21, 2011

trim white space · 73ec4a49

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15774 ee4ac58c-ac51-4696-9907-e4b3aa274f04

73ec4a49

Mar 10, 2011

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

Mar 09, 2011

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

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

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

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

Nov 10, 2010

fix for concat · 8f4b9c5f

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14994 ee4ac58c-ac51-4696-9907-e4b3aa274f04

8f4b9c5f

Nov 02, 2010

fix for zero insert size · a8467866

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14956 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a8467866

show orientation and zero size inserts · 994db9c7

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14948 ee4ac58c-ac51-4696-9907-e4b3aa274f04

994db9c7

Oct 25, 2010

fix strand stack view using colour by coverage · 6ce69cf4

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14920 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6ce69cf4

Oct 24, 2010

speed up check for multiple blocks in cigar · 35ccf025

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14915 ee4ac58c-ac51-4696-9907-e4b3aa274f04

35ccf025

Oct 21, 2010

draw alignment blocks to show splits in reads over introns · f95df8c3

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14894 ee4ac58c-ac51-4696-9907-e4b3aa274f04

f95df8c3

Sep 23, 2010

use FeatureContigPredicate to match reads to reference contig · e77a1c9a

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14780 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e77a1c9a

Sep 09, 2010

fix for snp and coverage plots when zooming in · 24381086

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14734 ee4ac58c-ac51-4696-9907-e4b3aa274f04

24381086

Jul 07, 2010

changes to integrate vcf view into artemis · 6c76aa8d

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14161 ee4ac58c-ac51-4696-9907-e4b3aa274f04

6c76aa8d

Jun 30, 2010

fix for zoomed in nucleotide view showing reads with gaps joined by lines · a6bc0eea

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14129 ee4ac58c-ac51-4696-9907-e4b3aa274f04

a6bc0eea

Jun 25, 2010

change FileSystemDialog constructor to provide the program name and file type · 43bdca7a

tjc authored 14 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14114 ee4ac58c-ac51-4696-9907-e4b3aa274f04

43bdca7a

Jun 15, 2010
- fix in the reporting of the position of insertions when there are previous deletions in a read · 85e35700
  tjc authored 15 years ago
  
  git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14029 ee4ac58c-ac51-4696-9907-e4b3aa274f04
  85e35700
May 26, 2010

test and warn for flipping sequences in Artemis · cc6883e6

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13905 ee4ac58c-ac51-4696-9907-e4b3aa274f04

cc6883e6

May 20, 2010

fix joining pairs on different reference sequences · 175432e1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13871 ee4ac58c-ac51-4696-9907-e4b3aa274f04

175432e1

May 18, 2010

fix SAMRecordPositionComparator by looking up offset · dce13c3a

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13861 ee4ac58c-ac51-4696-9907-e4b3aa274f04

dce13c3a

fix to draw connections in paired stack view when concatenating multiple contigs · 4b193746

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13858 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4b193746

fix for scale when selecting reference sequence · 968440fb

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13857 ee4ac58c-ac51-4696-9907-e4b3aa274f04

968440fb

May 13, 2010

set maximum rows visible for list of reference names · 4a90ddaf

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13818 ee4ac58c-ac51-4696-9907-e4b3aa274f04

4a90ddaf

May 12, 2010

fix · c6f3a571

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13817 ee4ac58c-ac51-4696-9907-e4b3aa274f04

c6f3a571

update macosx file drop · 34cacab1

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13816 ee4ac58c-ac51-4696-9907-e4b3aa274f04

34cacab1

additions for MacOSX about, quit · 65d77c46

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13814 ee4ac58c-ac51-4696-9907-e4b3aa274f04

65d77c46

Apr 29, 2010

fix details view for single reads · e026e75c

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13766 ee4ac58c-ac51-4696-9907-e4b3aa274f04

e026e75c

Mar 10, 2010

make stack view the default · 79342b21

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13453 ee4ac58c-ac51-4696-9907-e4b3aa274f04

79342b21

Mar 09, 2010

add SNP graph · b0c7373e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13445 ee4ac58c-ac51-4696-9907-e4b3aa274f04

b0c7373e

Mar 02, 2010

colour reads by coverage plot colour · aea0aa1e

tjc authored 15 years ago

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13371 ee4ac58c-ac51-4696-9907-e4b3aa274f04

aea0aa1e

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