Commits · 1cc57f14f247eb766ba69ca7f09a66854f42f965 · violethaze74 / Artemis

Jun 12, 2012
- fix for the initial display of reads mapped to short sequences · 1cc57f14
  tcarver authored 13 years ago
  
  1cc57f14
- add colour to BAM menu to identify read colours · 019e5222
  tcarver authored 13 years ago
  
  019e5222
Jun 11, 2012
- fix for creating BAM index · 365c7cc1
  tcarver authored 13 years ago
  
  365c7cc1
Jun 06, 2012
- in nucleotide view keep reference sequence visible at the top of the · cd7874f5
  tcarver authored 13 years ago
  cd7874f5
Jun 01, 2012
- highlight paired-stack connection link when selected · 453e9b26
  tcarver authored 13 years ago
  
  453e9b26
- improve paired stack view with multiple BAM files · 9c510db8
  tcarver authored 13 years ago
  
  9c510db8
Apr 10, 2012
- use ReadCountDialog · 4574a3aa
  tcarver authored 13 years ago
  
  4574a3aa
Apr 05, 2012
- loading cram class · c4758524
  tcarver authored 13 years ago
  
  c4758524
- fix in getMate() · de89f0e0
  tcarver authored 13 years ago
  
  de89f0e0
Mar 29, 2012
- use hashmap and preliminary cram support · 71caa686
  tcarver authored 13 years ago
  
  71caa686
Feb 13, 2012
- VALIDATION_STRINGENCY=SILENT · c93ceadf
  tcarver authored 13 years ago
  
  c93ceadf
- set VALIDATION_STRINGENCY=LENIENT · 4657921f
  tcarver authored 13 years ago
  
  4657921f
Feb 10, 2012
- set viewport position for the strand view when changing resolution · 61798fc2
  tcarver authored 13 years ago
  
  61798fc2
Jan 20, 2012
- fix for repainting snp and coverage plot when zoomed in · 05a0940c
  tcarver authored 13 years ago
  
  05a0940c
Dec 01, 2011
- throw SAMException if BAM index not present · 814937f3
  tcarver authored 13 years ago
  
  814937f3
Nov 30, 2011
- set a limit to MAX_RECORDS_IN_RAM for picard · 2b6e3ccc
  tcarver authored 13 years ago
  
  2b6e3ccc
- provide command line if index file not found and picard fails to index · 4b120c8e
  tcarver authored 13 years ago
  4b120c8e
- if the BAM index is not present try to use picard to index the file · 8497c589
  tcarver authored 13 years ago
  
  8497c589
Sep 28, 2011
- fix opening multiple BamView windows · a8db3887
  tcarver authored 13 years ago
  
  a8db3887
Sep 26, 2011
- fix for opening additional BAM's · 3e554097
  tcarver authored 13 years ago
  
  3e554097
- fix for graph repainting in standalone bamview · 3f67a3af
  tcarver authored 13 years ago
  
  3f67a3af
Sep 08, 2011
- fix for cloned BamView windows to have independent list of BAM files · bf20aa09
  tcarver authored 13 years ago
  
  bf20aa09
- add close option for individual BamView window · bd483cda
  tcarver authored 13 years ago
  
  bd483cda
Aug 18, 2011
- typo fix · 9626651b
  tcarver authored 13 years ago
  
  9626651b
- use a non-modal dialog to report change of reference sequence · 846f8f7c
  tcarver authored 13 years ago
  
  846f8f7c
Aug 16, 2011
- add read name to exception in showSNPsOnReads() · 364b4c48
  tcarver authored 13 years ago
  
  364b4c48
Aug 10, 2011
- changes for SAMRecordList · 4cbb60ac
  tcarver authored 13 years ago
  
  4cbb60ac
Aug 09, 2011
- more SAM record list · f1867d40
  tcarver authored 13 years ago
  
  f1867d40
Aug 08, 2011
- sam record list · 85023bb0
  tcarver authored 13 years ago
  
  85023bb0
- colour reads read if pair are same orientation · 16696e09
  tcarver authored 13 years ago
  
  16696e09
Aug 04, 2011
- start on a read list · cd11337a
  tcarver authored 13 years ago
  
  cd11337a
Aug 02, 2011
- add mate attributes to read details display · 05fd8694
  tcarver authored 13 years ago
  
  05fd8694
Aug 01, 2011
- fix for drawing connections between read pairs in inferred size view · deb870cd
  tcarver authored 13 years ago
  deb870cd
Jun 15, 2011
- optionally include mapped reads to all reference sequences in RPKM calculation · 73b39082
  tjc authored 14 years ago
  73b39082
Jun 07, 2011
- auto-completion for reference sequence selection · a28d2329
  tjc authored 14 years ago
  a28d2329
May 31, 2011
- BamView checks the sequence length matches the BAM header (SQ) length · 319794b7
  tjc authored 14 years ago
  319794b7
May 13, 2011
- use FTPSeekableStream to support BAM files over FTP · 1f3cb4cf
  tjc authored 14 years ago
  1f3cb4cf
Apr 21, 2011
- use progress bar for read count calculation · 9bf4f570
  tjc authored 14 years ago
  9bf4f570
Apr 20, 2011
- disable analyse menus when no FeatureDisplay · f0e143bf
  tjc authored 14 years ago
  f0e143bf
Apr 14, 2011
- rpkm changes · ac0c3909
  tjc authored 14 years ago
  ac0c3909

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