Commits · f933e38992ce7fb059800951e0179578a4b3b661 · violethaze74 / Artemis

Sep 28, 2012
- add coverage heatmap · f933e389
  tcarver authored 12 years ago
  
  f933e389
Sep 17, 2012
- fix for hiding BAM's · 9e460449
  tcarver authored 12 years ago
  
  9e460449
Sep 14, 2012
- add listener to update reference sequence · 81450504
  tcarver authored 12 years ago
  
  81450504
Sep 11, 2012
- define SNP arraylist as List · 4a404267
  tcarver authored 12 years ago
  
  4a404267
- use getSNPs() to get SNP positions so when showing SNPs the duplicate · 12563cab
  tcarver authored 12 years ago
  
  reads are displayed separately in stack view
  12563cab
Sep 07, 2012
- introduce threading and max read coverage threshold · 28bc5f0d
  tcarver authored 12 years ago
  
  28bc5f0d
Aug 31, 2012
- tidy · 8200f192
  tcarver authored 12 years ago
  
  8200f192
Aug 30, 2012
- use BamViewRecord to store BAM index rather than setting SAMRecord · 204eb711
  tcarver authored 12 years ago
  
  attribute
  204eb711
Aug 15, 2012
- parsing of the header happens during SAMFileReader construction, so need · a7d739a3
  tcarver authored 12 years ago
  
  to set the default stringency
  a7d739a3
Aug 09, 2012
- disable analyse option if there is no feature display · 5cf4bd24
  tcarver authored 12 years ago
  
  5cf4bd24
Aug 08, 2012
- changes to allow the use of BAM file grouping when creating features · 5142f826
  tcarver authored 12 years ago
  
  5142f826
Aug 03, 2012
- add option to create new features where the read count is seen in a · b94fa291
  tcarver authored 12 years ago
  
  minimum number of BAM files
  b94fa291
Jul 27, 2012
- add coverage by strand option to views menu · 76f5ac26
  tcarver authored 12 years ago
  
  76f5ac26
Jul 24, 2012
- set viewport position when switching to coverage plot · 9c938f52
  tcarver authored 12 years ago
  
  9c938f52
Jul 17, 2012
- define BAM_SUFFIX pattern · a61c6c63
  tcarver authored 12 years ago
  
  a61c6c63
Jul 11, 2012
- provide options for threshold and minimum feature size for creating · a5f7f9d5
  tcarver authored 12 years ago
  
  features from coverage
  a5f7f9d5
Jul 10, 2012
- adding create features option · db03f478
  tcarver authored 12 years ago
  
  db03f478
Jul 04, 2012
- fix for concatenated sequences in a different order to the BAM header · ac67866c
  tcarver authored 12 years ago
  
  ac67866c
- fix for warning message in linux · bc17906f
  tcarver authored 12 years ago
  
  bc17906f
Jun 21, 2012
- add option to switch the coverage graph to plot by the strand · 067e8216
  tcarver authored 12 years ago
  
  067e8216
Jun 18, 2012
- highlight selection range on graphs · 5eb0d1c8
  tcarver authored 12 years ago
  
  5eb0d1c8
Jun 15, 2012
- add option for grouping bam's · 177243de
  tcarver authored 12 years ago
  
  177243de
Jun 12, 2012
- fix for the initial display of reads mapped to short sequences · 1cc57f14
  tcarver authored 12 years ago
  
  1cc57f14
- add colour to BAM menu to identify read colours · 019e5222
  tcarver authored 12 years ago
  
  019e5222
Jun 11, 2012
- fix for creating BAM index · 365c7cc1
  tcarver authored 12 years ago
  
  365c7cc1
Jun 06, 2012
- in nucleotide view keep reference sequence visible at the top of the · cd7874f5
  tcarver authored 12 years ago
  
  panel
  cd7874f5
Jun 01, 2012
- highlight paired-stack connection link when selected · 453e9b26
  tcarver authored 12 years ago
  
  453e9b26
- improve paired stack view with multiple BAM files · 9c510db8
  tcarver authored 12 years ago
  
  9c510db8
Apr 10, 2012
- use ReadCountDialog · 4574a3aa
  tcarver authored 12 years ago
  
  4574a3aa
Apr 05, 2012
- loading cram class · c4758524
  tcarver authored 12 years ago
  
  c4758524
- fix in getMate() · de89f0e0
  tcarver authored 12 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
  
  the BAM
  4b120c8e
- if the BAM index is not present try to use picard to index the file · 8497c589
  tcarver authored 13 years ago
  
  8497c589

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