diff --git a/doc/GATK_Hello_World.pdf b/doc/GATK_Hello_World.pdf index 4a1aefc9e..0331cc804 100755 Binary files a/doc/GATK_Hello_World.pdf and b/doc/GATK_Hello_World.pdf differ diff --git a/doc/GATK_Hello_World.tex b/doc/GATK_Hello_World.tex index 1a5c25431..0651ab94c 100755 --- a/doc/GATK_Hello_World.tex +++ b/doc/GATK_Hello_World.tex @@ -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 should not start with a package declaration). \item It must subclass one of the basic walkers in the - org.broadinstitute.sting.gatk.walkers package: BasicReadWalker or - BasicLociWalker. + org.broadinstitute.sting.gatk.walkers package: ReadWalker or + LociWalker. \item It must live in the directory \$STING\_HOME/dist/walkers. \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 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 * . */ -public class HelloWalker extends BasicReadWalker { +public class HelloWalker extends ReadWalker { private Long currentRead = 0L; // Maps each read to the value 1.