Commit 1899493e authored by tcarver's avatar tcarver
Browse files

add bam clone options

parent b26b6415
......@@ -52,6 +52,29 @@ using these file types). This can take a path name to a file or an HTTP address.
</PARA>
</SECT2>
<SECT2 ID="JVM-NG2">
<TITLE><LITERAL>-Dbam1=pathToFile1 -Dbam2=pathToFile2</LITERAL></TITLE>
<PARA>
The following will open BAM files in separate panels (using -Dbam[1,2,3...]):
</PARA>
<PARA>
<COMMAND>art -Dbam1=fileA.bam -Dbam2=fileB.bam</COMMAND>
</PARA>
</SECT2>
<SECT2 ID="JVM-NG3">
<TITLE><LITERAL>-DbamClone=n</LITERAL></TITLE>
<PARA>
Multiple BAM panels can be opened using the bamClone flag this is used with the -Dbam flag:
</PARA>
<PARA>
<COMMAND>art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n</COMMAND>
</PARA>
<PARA>
(where n is an integer greater than 1). All BAM files are then shown in each panel.
</PARA>
</SECT2>
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
......
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