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<SECT2 ID="JVMOPTS-MEM">
<TITLE><LITERAL>-Xmsn -Xmxn</LITERAL></TITLE>
<PARA>
Use <LITERAL>-Xmsn</LITERAL> to specify the initial size, in bytes, of the
memory allocation pool. This value must be a multiple of 1024 greater than
1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate
megabytes.
</PARA>
<PARA>
Use <LITERAL>-Xmxn</LITERAL> to specify the maximum size, in bytes, of the
memory allocation pool. This value must a multiple of 1024 greater than
2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate
megabytes.
</PARA>
</SECT2>
<SECT2 ID="BB-MODE">
<TITLE><LITERAL>-Dblack_belt_mode=false</LITERAL></TITLE>
<PARA>
If this is set to false then warning messages are kept to a minimum.
</PARA>
</SECT2>
<SECT2 ID="JVM-OFFSET">
<TITLE><LITERAL>-Doffset=10000</LITERAL></TITLE>
<PARA>
This sets the base position that &prog; opens at, e.g. 10000.
</PARA>
</SECT2>
<SECT2 ID="JVM-USERPLOT">
<TITLE><LITERAL>-Duserplot=pathToFile</LITERAL></TITLE>
<PARA>
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">
<TITLE><LITERAL>-Dloguserplot=pathToFile</LITERAL></TITLE>
<PARA>
This is the same as the above userplot option except that the log transform of the data is plotted.
</PARA>
</SECT2>
<![ %artemis-only; [
<SECT2 ID="JVM-NG">
<TITLE><LITERAL>-Dbam=pathToFile</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.
</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>
]]>
<![ %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-SHOW-SNPS">
<TITLE><LITERAL>-Dshow_snps</LITERAL></TITLE>
<PARA>
Show SNP marks in BAM panels.
</PARA>
</SECT2>
<SECT2 ID="JVM-SHOW-SNPS-PLOT">
<TITLE><LITERAL>-Dshow_snp_plot</LITERAL></TITLE>
<PARA>
Automatically open SNP plots for BAM files that are opened.
</PARA>
</SECT2>
<SECT2 ID="JVM-SHOW-COV-PLOT">
<TITLE><LITERAL>-Dshow_cov_plot</LITERAL></TITLE>
<PARA>
Automatically open coverage plots for BAM files that are opened.
</PARA>
</SECT2>
<SECT2 ID="JVM-CHADO">
<TITLE><LITERAL>-Dchado="hostname:port/database?username"</LITERAL></TITLE>
<PARA>
This is used to get &prog; to look for the database. The address of the database
(hostname, port and name) can be conveniently included
(e.g. -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro") and
these details are then the default database address in the popup login window.
</PARA>
</SECT2>
<SECT2 ID="JVM-CHADO-READONLY">
<TITLE><LITERAL>-Dread_only</LITERAL></TITLE>
<PARA>
For a read only chado connection -Dread_only is specified on the command line
(e.g. art -Dchado="genedb-db.sanger.ac.uk:5432/snapshot?genedb_ro" -Dread_only).
</PARA>
</SECT2>
<SECT2 ID="JVM-FWD-LINES">
<TITLE><LITERAL>-Dshow_forward_lines=false</LITERAL></TITLE>
<PARA>
Hide/show forward frame lines.
</PARA>
</SECT2>
<SECT2 ID="JVM-BWD-LINES">
<TITLE><LITERAL>-Dshow_reverse_lines=false</LITERAL></TITLE>
<PARA>
Hide/show reverse frame lines.
</PARA>
</SECT2>