diff --git a/extras/run-HLA b/bwakit/run-HLA similarity index 100% rename from extras/run-HLA rename to bwakit/run-HLA diff --git a/extras/run-bwamem b/bwakit/run-bwamem similarity index 100% rename from extras/run-bwamem rename to bwakit/run-bwamem diff --git a/extras/run-gen-ref b/bwakit/run-gen-ref similarity index 100% rename from extras/run-gen-ref rename to bwakit/run-gen-ref diff --git a/extras/typeHLA-selctg.js b/bwakit/typeHLA-selctg.js similarity index 100% rename from extras/typeHLA-selctg.js rename to bwakit/typeHLA-selctg.js diff --git a/extras/typeHLA.js b/bwakit/typeHLA.js similarity index 100% rename from extras/typeHLA.js rename to bwakit/typeHLA.js diff --git a/extras/typeHLA.sh b/bwakit/typeHLA.sh similarity index 100% rename from extras/typeHLA.sh rename to bwakit/typeHLA.sh diff --git a/extras/alt-demo.graffle b/extras/alt-demo.graffle deleted file mode 100644 index 32a8f5fe..00000000 --- a/extras/alt-demo.graffle +++ /dev/null @@ -1,330 +0,0 @@ - - - - - ActiveLayerIndex - 0 - ApplicationVersion - - com.omnigroup.OmniGraffle - 139.18.0.187838 - - AutoAdjust - - BackgroundGraphic - - Bounds - {{0, 0}, {576, 733}} - Class - SolidGraphic - ID - 2 - Style - - shadow - - Draws - NO - - stroke - - Draws - NO - - - - BaseZoom - 0 - CanvasOrigin - {0, 0} - ColumnAlign - 1 - ColumnSpacing - 36 - CreationDate - 2014-11-17 16:51:42 +0000 - Creator - Heng Li - DisplayScale - 1 0/72 in = 1 0/72 in - GraphDocumentVersion - 8 - GraphicsList - - - Bounds - {{35.699992179870605, 151.89999580383301}, {476, 224}} - Class - ShapedGraphic - FitText - YES - Flow - Resize - FontInfo - - Font - AndaleMono - Size - 12 - - ID - 28 - Shape - Rectangle - Style - - fill - - Draws - NO - - shadow - - Draws - NO - - stroke - - Draws - NO - - - Text - - Align - 0 - Pad - 0 - Text - {\rtf1\ansi\ansicpg1252\cocoartf1265\cocoasubrtf210 -\cocoascreenfonts1{\fonttbl\f0\fnil\fcharset0 Consolas;\f1\fnil\fcharset0 Consolas-Bold;} -{\colortbl;\red255\green255\blue255;\red0\green0\blue0;\red127\green127\blue127;\red255\green0\blue0; -\red204\green204\blue204;\red0\green0\blue255;\red0\green128\blue0;\red255\green128\blue0;} -\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural - -\f0\fs24 \cf2 Read: A\cf0 TCAGCATC\ -\cf2 \ - ALT ctg 1: \cf3 TGA\cf3 AA---CGAATGCAAATGGTCA -\f1\b \cf4 ATCAGCATC -\f0\b0 \cf3 GAACTAGTCACAT\cf2 \ - \cf3 |||||\cf5 (high div) \cf3 ||||||\cf5 (novel ins)\cf3 ||||||||||\cf2 \ -Chromosome:\cf3 GCGTACATGATACGA -\f1\b \cf6 ATCgGCATC -\f0\b0 \cf3 ATGGTC-------------CTAGTCACATCGTAATC\ -\cf2 \cf3 |||||||||||| ||||||||||\cf5 (novel ins) \cf3 ||||||||||\ -\cf2 ALT ctg 2:\cf3 TGATACGA -\f1\b \cf7 ATCgcCATC -\f0\b0 \cf3 ATGGTCA -\f1\b \cf8 ATCgcCAgC -\f0\b0 \cf3 GAACTAGTCACAT\ -\ -\cf2 4 potential hits: -\f1\b \cf4 ATCAGCATC -\f0\b0 \cf0 > -\f1\b \cf6 ATCgGCATC -\f0\b0 \cf0 > -\f1\b \cf7 ATCgcCATC -\f0\b0 \cf2 > -\f1\b \cf8 ATCgcCAgC\ -\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural - -\f0\b0 \cf0 2 hit groups: \{ -\f1\b \cf4 ATCAGCATC -\f0\b0 \cf0 , -\f1\b \cf8 ATCgcCAgC -\f0\b0 \cf2 \} and\cf0 \{ -\f1\b \cf6 ATCgGCATC -\f0\b0 \cf2 , -\f1\b \cf7 ATCgcCATC -\f0\b0 \cf2 \}\ -\cf0 Hits considered in mapQ: -\f1\b \cf4 ATCAGCATC -\f0\b0 \cf0 and -\f1\b \cf6 ATCgGCATC -\f0\b0 \cf2 (best from each group) -\f1\b \cf6 \ -\pard\tx560\tx1120\tx1680\tx2240\tx2800\tx3360\tx3920\tx4480\tx5040\tx5600\tx6160\tx6720\pardirnatural - -\f0\b0 \cf3 \ -\cf2 In the output SAM: -\f1\b \cf6 ATCgGCATC -\f0\b0 \cf2 as the primary SAM line with mapQ=0\ - -\f1\b \cf4 ATCAGCATC -\f0\b0 \cf2 as a supplementary line with mapQ>0\ - -\f1\b \cf8 ATCgcCAgC -\f0\b0 \cf2 as a supplementary line with mapQ>0\ - -\f1\b \cf7 ATCgcCATC -\f0\b0 \cf2 in an XA tag, not as a separate line} - VerticalPad - 0 - - Wrap - NO - - - GridInfo - - GridSpacing - 7.1999998092651367 - MajorGridSpacing - 10 - SnapsToGrid - YES - - GuidesLocked - NO - GuidesVisible - YES - HPages - 1 - ImageCounter - 1 - KeepToScale - - Layers - - - Lock - NO - Name - Layer 1 - Print - YES - View - YES - - - LayoutInfo - - Animate - NO - circoMinDist - 18 - circoSeparation - 0.0 - layoutEngine - dot - neatoSeparation - 0.0 - twopiSeparation - 0.0 - - LinksVisible - NO - MagnetsVisible - NO - MasterSheets - - ModificationDate - 2014-11-17 18:28:10 +0000 - Modifier - Heng Li - NotesVisible - NO - Orientation - 2 - OriginVisible - NO - PageBreaks - YES - PrintInfo - - NSBottomMargin - - float - 41 - - NSHorizonalPagination - - coded - BAtzdHJlYW10eXBlZIHoA4QBQISEhAhOU051bWJlcgCEhAdOU1ZhbHVlAISECE5TT2JqZWN0AIWEASqEhAFxlwCG - - NSLeftMargin - - float - 18 - - NSPaperSize - - size - {612, 792} - - NSPrintReverseOrientation - - int - 0 - - NSRightMargin - - float - 18 - - NSTopMargin - - float - 18 - - - PrintOnePage - - ReadOnly - NO - RowAlign - 1 - RowSpacing - 36 - SheetTitle - Canvas 1 - SmartAlignmentGuidesActive - YES - SmartDistanceGuidesActive - YES - UniqueID - 1 - UseEntirePage - - VPages - 1 - WindowInfo - - CurrentSheet - 0 - ExpandedCanvases - - - name - Canvas 1 - - - Frame - {{367, 6}, {710, 872}} - ListView - - OutlineWidth - 142 - RightSidebar - - ShowRuler - - Sidebar - - SidebarWidth - 120 - VisibleRegion - {{0, 0}, {575, 733}} - Zoom - 1 - ZoomValues - - - Canvas 1 - 1 - 1 - - - - - diff --git a/extras/alt-demo.png b/extras/alt-demo.png deleted file mode 100644 index 71f49763..00000000 Binary files a/extras/alt-demo.png and /dev/null differ