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Minor doc fixes

This commit is contained in:
Eric Banks 2011-08-16 12:55:45 -04:00
parent 125ad0bcfa
commit ab0b56ed11
3 changed files with 11 additions and 11 deletions
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2
public/java/src/org/broadinstitute/sting/commandline/Output.java
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@ -55,7 +55,7 @@ public @interface Output {
* --help argument is specified. * --help argument is specified.
* @return Doc string associated with this command-line argument. * @return Doc string associated with this command-line argument.
*/ */
String doc() default "An output file presented to the walker. Will overwrite contents if file exists."; String doc() default "An output file created by the walker. Will overwrite contents if file exists";
/** /**
* Is this argument required. If true, the command-line argument system will * Is this argument required. If true, the command-line argument system will

10
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -84,7 +84,7 @@ import java.util.*;
* </ol> * </ol>
* <p> * <p>
* An important note: the input bam(s), reference, and known indel file(s) should be the same ones used for the RealignerTargetCreator step. * An important note: the input bam(s), reference, and known indel file(s) should be the same ones used for the RealignerTargetCreator step.
* * <p>
* Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them * Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them
* (or with reads from similar technologies). * (or with reads from similar technologies).
* *
@ -101,11 +101,11 @@ import java.util.*;
* <h2>Examples</h2> * <h2>Examples</h2>
* <pre> * <pre>
* java -Xmx4g -jar GenomeAnalysisTK.jar \ * java -Xmx4g -jar GenomeAnalysisTK.jar \
* -I <input.bam> \ * -I input.bam \
* -R <ref.fasta> \ * -R ref.fasta \
* -T IndelRealigner \ * -T IndelRealigner \
* -targetIntervals <intervalListFromRTC.intervals> \ * -targetIntervals intervalListFromRTC.intervals \
* -o <realignedBam.bam> \ * -o realignedBam.bam \
* [--known /path/to/indels.vcf] \ * [--known /path/to/indels.vcf] \
* [-compress 0] (this argument recommended to speed up the process *if* this is only a temporary file; otherwise, use the default value) * [-compress 0] (this argument recommended to speed up the process *if* this is only a temporary file; otherwise, use the default value)
* </pre> * </pre>

10
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -52,7 +52,7 @@ import java.util.Collections;
import java.util.List; import java.util.List;
/** /**
* Emits intervals for the Local Indel Realigner to target for cleaning. * Emits intervals for the Local Indel Realigner to target for realignment.
* *
* <p> * <p>
* The local realignment tool is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases * The local realignment tool is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases
@ -72,7 +72,7 @@ import java.util.List;
* </ol> * </ol>
* <p> * <p>
* An important note: the input bam(s), reference, and known indel file(s) should be the same ones to be used for the IndelRealigner step. * An important note: the input bam(s), reference, and known indel file(s) should be the same ones to be used for the IndelRealigner step.
* * <p>
* Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them * Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them
* (or with reads from similar technologies). This tool also ignores MQ0 reads and reads with consecutive indel operators in the CIGAR string. * (or with reads from similar technologies). This tool also ignores MQ0 reads and reads with consecutive indel operators in the CIGAR string.
* *
@ -89,10 +89,10 @@ import java.util.List;
* <h2>Examples</h2> * <h2>Examples</h2>
* <pre> * <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \
* -I <input.bam> \ * -I input.bam \
* -R <ref.fasta> \ * -R ref.fasta \
* -T RealignerTargetCreator \ * -T RealignerTargetCreator \
* -o <forIndelRealigner.intervals> \ * -o forIndelRealigner.intervals \
* [--known /path/to/indels.vcf] * [--known /path/to/indels.vcf]
* </pre> * </pre>
* *