Commit ed5d96d4 authored by tcarver's avatar tcarver
Browse files

add act options

parent bf8bec1d
......@@ -34,6 +34,15 @@ This sets the base position that &prog; opens at, e.g. 10000.
This can be used to open userplots from the command line. The paths are comma
separated to open multiple plots (-Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2').
</PARA>
<![ %act-only; [
<PARA>
In ACT numbers are used to associate the file with a particular sequence. For example to add a
userplot to the second sequence:
</PARA>
<PARA><COMMAND>act -Duserplot2=/pathToFile/userPlot</COMMAND></PARA>
]]>
</SECT2>
<SECT2 ID="JVM-LOGUSERPLOT">
......@@ -44,6 +53,7 @@ This is the same as the above userplot option except that the log transform of t
</SECT2>
<![ %artemis-only; [
<SECT2 ID="JVM-NG">
<TITLE><LITERAL>-Dbam=pathToFile</LITERAL></TITLE>
<PARA>
......@@ -52,7 +62,6 @@ using these file types). This can take a path name to a file or an HTTP address.
</PARA>
</SECT2>
<![ %artemis-only; [
<SECT2 ID="JVM-NG2">
<TITLE><LITERAL>-Dbam1=pathToFile1 -Dbam2=pathToFile2</LITERAL></TITLE>
<PARA>
......@@ -77,6 +86,19 @@ Multiple BAM panels can be opened using the bamClone flag this is used with the
</SECT2>
]]>
<![ %act-only; [
<SECT2 ID="JVM-NG2">
<TITLE><LITERAL>-Dbam1=pathToFile1 -Dbam2=pathToFile2</LITERAL></TITLE>
<PARA>
This can be used to open BAM files and/or VCF/BCF files (see <XREF LINKEND="FILEMENU-READ-BAM"> for more about the
using these file types). This can take a path name to a file or an HTTP address.
Numbers are used to associate the file with a particular sequence. For example to add a BAM to the
first (top) sequence in ACT:
</PARA>
<PARA><COMMAND>act -Dbam1=/pathToFile/file.bam </COMMAND></PARA>
</SECT2>
]]>
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
......
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