Commits · df7ccbf5ff03d7a5c49aee582f0d856ab5d53c07 · violethaze74 / Artemis

Oct 23, 2017

Initial BAM View changes to fix selection issues, zooming into secondary... · df7ccbf5

“kpepper” authored 7 years ago

Initial BAM View changes to fix selection issues, zooming into secondary alignments, erroneous collapsing of reads with same start/end position and display of SNPs - related to RT ticket 597652

df7ccbf5

Mar 14, 2014
- fix for paired stack view when showing SNPs · f63e674b
  tcarver authored 11 years ago
  
  f63e674b
Mar 11, 2014
- refactor for read count and rpkm calculations · ee5910a1
  tcarver authored 11 years ago
  
  ee5910a1
Feb 18, 2014
- fixes for view positions · af4cc378
  tcarver authored 11 years ago
  
  af4cc378
Jan 24, 2014
- use new drawMax() for coverage plot · de7b3227
  tcarver authored 11 years ago
  
  de7b3227
Jan 14, 2014
- introduce separate log scale option for coverage plots · d0bc6843
  tcarver authored 11 years ago
  
  d0bc6843
Dec 13, 2013
- changed for read count and rpkm to take into account strand specific tag · f1285f33
  tcarver authored 11 years ago
  
  f1285f33
Sep 09, 2013
- fix for when FeatureDisplay is not used · e4f5b4dc
  tcarver authored 11 years ago
  
  e4f5b4dc
May 03, 2013
- fix for zoomed in base view · 65b979ad
  tcarver authored 11 years ago
  
  65b979ad
Apr 30, 2013
- adjustable read line height · 09441f80
  tcarver authored 11 years ago
  
  09441f80
Apr 29, 2013
- fix ReadGroupsFrame · 9a5fa4a8
  tcarver authored 11 years ago
  
  9a5fa4a8
Apr 26, 2013
- use read group information · 60b2d2a2
  tcarver authored 11 years ago
  
  60b2d2a2
Apr 19, 2013
- fix strand stack view with RNASeq strand specific option checked · 7f102fc7
  tcarver authored 11 years ago
  
  7f102fc7
Apr 18, 2013
- use local EntryEdit in openBamView() · 30a5f046
  tcarver authored 11 years ago
  
  30a5f046
- add index reference listener in openBamView() · 615a729b
  tcarver authored 11 years ago
  
  615a729b
- fix for colour by strand option when XS tag is missing · 3d014d08
  tcarver authored 11 years ago
  
  3d014d08
Apr 12, 2013
- add rnaseq strand specific option · 387adfd0
  tcarver authored 11 years ago
  
  387adfd0
Mar 21, 2013
- add command line VM options show_snps, show_snp_plot, show_cov_plot · e6fa5e49
  tcarver authored 12 years ago
  
  e6fa5e49
Mar 07, 2013
- show read mate sequence if available · 15355f51
  tcarver authored 12 years ago
  
  15355f51
Feb 15, 2013
- fix SNPs for CRAM · 024d1180
  tcarver authored 12 years ago
  
  024d1180
Feb 14, 2013
- set log level · 7bc6ee93
  tcarver authored 12 years ago
  
  7bc6ee93
Feb 08, 2013
- add a log statement · f5e4a995
  tcarver authored 12 years ago
  
  f5e4a995
Feb 07, 2013
- fix for threshold cut-off · 7929dd0e
  tcarver authored 12 years ago
  
  7929dd0e
Jan 10, 2013
- fix for automatically switching to coverage plot when zooming out · 0c391db8
  tcarver authored 12 years ago
  
  0c391db8
- change cloneBamView() to openBamView(List bamsList) · 9c57b2b7
  tcarver authored 12 years ago
  
  9c57b2b7
- add cloneBamView() · b0b7b4d3
  tcarver authored 12 years ago
  
  b0b7b4d3
Dec 11, 2012
- change group bam frame to get icon from menu · 2d1392df
  tcarver authored 12 years ago
  
  2d1392df
Nov 26, 2012
- add bamview image save option · 5c371ae9
  tcarver authored 12 years ago
  
  5c371ae9
Oct 30, 2012
- add coverage options menu · f92c6a70
  tcarver authored 12 years ago
  
  f92c6a70
Oct 29, 2012
- add heatmap options · c4265973
  tcarver authored 12 years ago
  
  c4265973
Oct 26, 2012
- select BAM file in heatmap view · 46f1f348
  tcarver authored 12 years ago
  
  46f1f348
Oct 25, 2012
- add tooltip to coverage heatmaps · 981c33b7
  tcarver authored 12 years ago
  
  981c33b7
Oct 24, 2012
- fixes for heatmap · c65931a7
  tcarver authored 12 years ago
  
  c65931a7
Oct 22, 2012
- add option for creating features from reads on opposite strand - for · 83759ef9
  tcarver authored 12 years ago
  
  single strand cDNA
  83759ef9
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

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