Merge branch 'master' into jsmithro_snpcoverage

Conflicts:
	main.css
	src/JBrowse/View/Track/Alignments.js

.gitignore

@@ -3,19 +3,21 @@
 .#*
 \#*\#
 *.index
-bin/wig2png
+/bin/wig2png
 *.pyc
 *TODO.txt
 Makefile
 /sample_data/json
-src/wig2png/config.log
-src/wig2png/config.status
-src/wig2png/src/config.h
-docs/jsdoc/
+/src/wig2png/config.log
+/src/wig2png/config.status
+/src/wig2png/src/config.h
+/docs/jsdoc/
 /*-debug.html
-jslib/dojo-release-*-src/
 /extlib/
 autom4te.cache
 sample_data/raw/tomato
-.prove
-*.sw*
+/.prove
+/setup.log
+/release-notes.html
+samtools/
+setup.log

.gitmodules

@@ -13,3 +13,15 @@
 [submodule "src/jszlib"]
 	path = src/jszlib
 	url = git://github.com/rbuels/jszlib.git
+[submodule "src/lazyload"]
+	path = src/lazyload
+	url = git://github.com/rbuels/lazyload.git
+[submodule "src/dgrid"]
+	path = src/dgrid
+	url = git://github.com/SitePen/dgrid.git
+[submodule "src/xstyle"]
+	path = src/xstyle
+	url = git://github.com/kriszyp/xstyle.git
+[submodule "src/put-selector"]
+	path = src/put-selector
+	url = git://github.com/kriszyp/put-selector.git

.htaccess

@@ -0,0 +1,10 @@
+# This Apache .htaccess file is for
+# allowing cross-origin requests as defined by the Cross-Origin
+# Resource Sharing working draft from the W3C
+# (http://www.w3.org/TR/cors/).  In order for Apache to pay attention
+# to this, it must have mod_headers enabled, and its AllowOverride
+# configuration directive must allow FileInfo overrides.
+<IfModule mod_headers.c>
+    Header onsuccess set Access-Control-Allow-Origin *
+    Header onsuccess set Access-Control-Allow-Headers X-Requested-With
+</IfModule>

Makefile.PL

@@ -40,12 +40,12 @@ my %WriteMakefileArgs = (
     "Bio::Root::Version" => "1.006000",
     "Bio::SeqFeature::Annotated" => 0,
     "Carp" => 0,
+    "Cache::Ref::FIFO" => 0,
     "Cwd" => 0,
     "DBI" => 0,
     "Data::Dumper" => 0,
     "Devel::Size" => 0,
     "Digest::Crc32" => 0,
-    "Digest::MurmurHash" => 0,
     "Exporter" => 0,
     "Fcntl" => 0,
     "File::Basename" => 0,
@@ -61,6 +61,7 @@ my %WriteMakefileArgs = (
     "Heap::Simple::XS" => 0,
     "IO::File" => 0,
     "JSON" => 2,
+    "JSON::XS" => 0,
     "List::Util" => 0,
     "POSIX" => 0,
     "PerlIO::gzip" => 0,

README.md

@@ -10,6 +10,7 @@ Make sure you have a web server installed on your development machine.  Any web
 
     cd /my/dev/webserver/root;
     git clone git@github.com:YOURACCOUNT/jbrowse.git
+    cd jbrowse
     git submodule update --init
     ./setup.sh
     # and now point your browser to