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IR should skip Ion reads just like it does with 454 reads; Tim has confirmed that official platform name for Ion.

This commit is contained in:
Eric Banks 2012-06-06 11:04:55 -04:00
parent b6a7c3f780
commit dd46d843fb
2 changed files with 19 additions and 7 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -532,8 +532,9 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
read.getMappingQuality() == 0 ||
read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) ||
ReadUtils.is454Read(read);
// TODO -- it would be nice if we could use indels from 454 reads as alternate consenses
ReadUtils.is454Read(read) ||
ReadUtils.isIonRead(read);
// TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses
}
private void cleanAndCallMap(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker, GenomeLoc readLoc) {

21
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -211,7 +211,7 @@ public class ReadUtils {
}
/**
* is the read a 454 read ?
* is the read a 454 read?
*
* @param read the read to test
* @return checks the read group tag PL for the default 454 tag
@ -221,7 +221,17 @@ public class ReadUtils {
}
/**
* is the read a SOLiD read ?
* is the read an IonTorrent read?
*
* @param read the read to test
* @return checks the read group tag PL for the default ion tag
*/
public static boolean isIonRead(SAMRecord read) {
return isPlatformRead(read, "IONTORRENT");
}
/**
* is the read a SOLiD read?
*
* @param read the read to test
* @return checks the read group tag PL for the default SOLiD tag
@ -231,7 +241,7 @@ public class ReadUtils {
}
/**
* is the read a SLX read ?
* is the read a SLX read?
*
* @param read the read to test
* @return checks the read group tag PL for the default SLX tag
@ -241,10 +251,11 @@ public class ReadUtils {
}
/**
* checks if the read has a platform tag in the readgroup equal to 'name' ?
* checks if the read has a platform tag in the readgroup equal to 'name'.
* Assumes that 'name' is upper-cased.
*
* @param read the read to test
* @param name the platform name to test
* @param name the upper-cased platform name to test
* @return whether or not name == PL tag in the read group of read
*/
public static boolean isPlatformRead(SAMRecord read, String name) {