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Fixed the Hello, World doc to reflect the collapse in the walker hierarchy. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@238 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-31 15:23:29 +00:00
parent 8e2ba7a294
commit d37d81822d
2 changed files with 5 additions and 5 deletions
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doc/GATK_Hello_World.pdf
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doc/GATK_Hello_World.tex
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@ -48,8 +48,8 @@ To be loaded by GATK, the walker must satisfy the following properties:
\item It must be in the unnamed package (in other words, the source \item It must be in the unnamed package (in other words, the source
should not start with a package declaration). should not start with a package declaration).
\item It must subclass one of the basic walkers in the \item It must subclass one of the basic walkers in the
org.broadinstitute.sting.gatk.walkers package: BasicReadWalker or org.broadinstitute.sting.gatk.walkers package: ReadWalker or
BasicLociWalker. LociWalker.
\item It must live in the directory \$STING\_HOME/dist/walkers. \item It must live in the directory \$STING\_HOME/dist/walkers.
\end{enumerate} \end{enumerate}
@ -65,13 +65,13 @@ Copy the following text into the file \$STING\_HOME/dist/walkers/HelloWalker.jav
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.BasicReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
/** /**
* Define a class extending from BasicReadWalker with types * Define a class extending from ReadWalker with types
* <MapType,ReduceType>. * <MapType,ReduceType>.
*/ */
public class HelloWalker extends BasicReadWalker<Integer,Long> { public class HelloWalker extends ReadWalker<Integer,Long> {
private Long currentRead = 0L; private Long currentRead = 0L;
// Maps each read to the value 1. // Maps each read to the value 1.