63 lines
1.4 KiB
Java
63 lines
1.4 KiB
Java
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package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.utils.StingException;
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/**
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* Support files for BWT.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class BWTFiles {
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/**
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* ANN (?) file name.
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*/
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public final String annFileName;
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/**
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* AMB (?) file name.
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*/
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public final String ambFileName;
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/**
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* Packed reference sequence file.
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*/
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public final String pacFileName;
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/**
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* Forward BWT file.
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*/
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public final String forwardBWTFileName;
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/**
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* Forward suffix array file.
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*/
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public final String forwardSAFileName;
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/**
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* Reverse BWT file.
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*/
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public final String reverseBWTFileName;
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/**
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* Reverse suffix array file.
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*/
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public final String reverseSAFileName;
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/**
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* Create a new BWA configuration file using the given prefix.
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* @param prefix Prefix to use when creating the configuration. Must not be null.
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*/
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public BWTFiles(String prefix) {
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if(prefix == null)
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throw new StingException("Prefix must not be null.");
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annFileName = prefix + ".ann";
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ambFileName = prefix + ".amb";
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pacFileName = prefix + ".pac";
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forwardBWTFileName = prefix + ".bwt";
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forwardSAFileName = prefix + ".sa";
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reverseBWTFileName = prefix + ".rbwt";
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reverseSAFileName = prefix + ".rsa";
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}
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}
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