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laying groundwork to have insertions and deletions going through the system.

This commit is contained in:
Mauricio Carneiro 2012-02-07 18:11:53 -05:00
parent 0d3ea0401c
commit e89887cd8e
2 changed files with 163 additions and 136 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
View File

@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.util.ArrayList;
import java.util.List;
@ -284,7 +285,7 @@ public class RecalDataManager {
public static void parseColorSpace(final GATKSAMRecord read) {
// If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
if (read.getReadGroup().getPlatform().toUpperCase().contains("SOLID")) {
if (ReadUtils.isSOLiDRead(read)) {
if (read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null) { // Haven't calculated the inconsistency array yet for this read
final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
if (attr != null) {
@ -382,7 +383,7 @@ public class RecalDataManager {
}
public static boolean checkNoCallColorSpace(final GATKSAMRecord read) {
if (read.getReadGroup().getPlatform().toUpperCase().contains("SOLID")) {
if (ReadUtils.isSOLiDRead(read)) {
final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
if (attr != null) {
byte[] colorSpace;
@ -611,21 +612,17 @@ public class RecalDataManager {
final Comparable[][] covariateValues_offset_x_covar = new Comparable[readLength][numRequestedCovariates];
final Comparable[] tempCovariateValuesHolder = new Comparable[readLength];
// Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
for (int i = 0; i < numRequestedCovariates; i++) {
for (int i = 0; i < numRequestedCovariates; i++) { // Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
requestedCovariates.get(i).getValues(gatkRead, tempCovariateValuesHolder, modelType);
for (int j = 0; j < readLength; j++) {
//copy values into a 2D array that allows all covar types to be extracted at once for
//an offset j by doing covariateValues_offset_x_covar[j]. This avoids the need to later iterate over covar types.
covariateValues_offset_x_covar[j][i] = tempCovariateValuesHolder[j];
}
for (int j = 0; j < readLength; j++)
covariateValues_offset_x_covar[j][i] = tempCovariateValuesHolder[j]; // copy values into a 2D array that allows all covar types to be extracted at once for an offset j by doing covariateValues_offset_x_covar[j]. This avoids the need to later iterate over covar types.
}
return covariateValues_offset_x_covar;
}
/**
* Perform a ceratin transversion (A <-> C or G <-> T) on the base.
* Perform a certain transversion (A <-> C or G <-> T) on the base.
*
* @param base the base [AaCcGgTt]
* @return the transversion of the base, or the input base if it's not one of the understood ones

134
public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -2,7 +2,6 @@ package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
/**
* BaseUtils contains some basic utilities for manipulating nucleotides.
*/
@ -29,21 +28,25 @@ public class BaseUtils {
byte b;
int index;
private Base(char base, int index) {
this.b = (byte) base;
this.index = index;
}
public byte getBase() { return b; }
public char getBaseAsChar() { return (char) b; }
public int getIndex() { return index; }
public boolean sameBase(byte o) { return b == o; }
public boolean sameBase(char o) { return b == (byte) o; }
public boolean sameBase(int i) { return index == i; }
}
// todo -- fix me (enums?)
public static final byte DELETION_INDEX = 4;
public static final byte NO_CALL_INDEX = 5; // (this is 'N')
@ -53,7 +56,6 @@ public class BaseUtils {
public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A');
public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T');
/// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
// a pyrimidine to another pyrimidine nucleotide (C <-> T).
// Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions.
@ -64,6 +66,7 @@ public class BaseUtils {
/**
* Returns the base substitution type of the 2 state SNP
*
* @param base1
* @param base2
* @return
@ -85,7 +88,9 @@ public class BaseUtils {
return !isTransition(base1, base2);
}
/** Private constructor. No instantiating this class! */
/**
* Private constructor. No instantiating this class!
*/
private BaseUtils() {}
static public boolean basesAreEqual(byte base1, byte base2) {
@ -96,7 +101,6 @@ public class BaseUtils {
return extendedBaseToBaseIndex(base1) == extendedBaseToBaseIndex(base2);
}
/**
* Converts a IUPAC nucleotide code to a pair of bases
*
@ -170,22 +174,26 @@ public class BaseUtils {
switch (base) {
case '*': // the wildcard character counts as an A
case 'A':
case 'a': return 0;
case 'a':
return 0;
case 'C':
case 'c': return 1;
case 'c':
return 1;
case 'G':
case 'g': return 2;
case 'g':
return 2;
case 'T':
case 't': return 3;
case 't':
return 3;
default: return -1;
default:
return -1;
}
}
/**
* Converts a simple base to a base index
*
@ -197,29 +205,37 @@ public class BaseUtils {
switch (base) {
case '*': // the wildcard character counts as an A
case 'A':
case 'a': return 0;
case 'a':
return 0;
case 'C':
case 'c': return 1;
case 'c':
return 1;
case 'G':
case 'g': return 2;
case 'g':
return 2;
case 'T':
case 't': return 3;
case 't':
return 3;
default: return -1;
default:
return -1;
}
}
static public int extendedBaseToBaseIndex(byte base) {
switch (base) {
case 'd':
case 'D': return DELETION_INDEX;
case 'D':
return DELETION_INDEX;
case 'n':
case 'N': return NO_CALL_INDEX;
case 'N':
return NO_CALL_INDEX;
default: return simpleBaseToBaseIndex(base);
default:
return simpleBaseToBaseIndex(base);
}
}
@ -232,11 +248,6 @@ public class BaseUtils {
return simpleBaseToBaseIndex(base) != -1;
}
@Deprecated
static public boolean isNBase(char base) {
return isNBase((byte)base);
}
static public boolean isNBase(byte base) {
return base == 'N' || base == 'n';
}
@ -249,11 +260,16 @@ public class BaseUtils {
*/
static public byte baseIndexToSimpleBase(int baseIndex) {
switch (baseIndex) {
case 0: return 'A';
case 1: return 'C';
case 2: return 'G';
case 3: return 'T';
default: return '.';
case 0:
return 'A';
case 1:
return 'C';
case 2:
return 'G';
case 3:
return 'T';
default:
return '.';
}
}
@ -270,11 +286,16 @@ public class BaseUtils {
*/
static public int crossTalkPartnerIndex(int baseIndex) {
switch (baseIndex) {
case 0: return 1; // A -> C
case 1: return 0; // C -> A
case 2: return 3; // G -> T
case 3: return 2; // T -> G
default: return -1;
case 0:
return 1; // A -> C
case 1:
return 0; // C -> A
case 2:
return 3; // G -> T
case 3:
return 2; // T -> G
default:
return -1;
}
}
@ -297,11 +318,16 @@ public class BaseUtils {
*/
static public byte complementIndex(int baseIndex) {
switch (baseIndex) {
case 0: return 3; // a -> t
case 1: return 2; // c -> g
case 2: return 1; // g -> c
case 3: return 0; // t -> a
default: return -1; // wtf?
case 0:
return 3; // a -> t
case 1:
return 2; // c -> g
case 2:
return 1; // g -> c
case 3:
return 0; // t -> a
default:
return -1; // wtf?
}
}
@ -314,14 +340,19 @@ public class BaseUtils {
static public byte simpleComplement(byte base) {
switch (base) {
case 'A':
case 'a': return 'T';
case 'a':
return 'T';
case 'C':
case 'c': return 'G';
case 'c':
return 'G';
case 'G':
case 'g': return 'C';
case 'g':
return 'C';
case 'T':
case 't': return 'A';
default: return base;
case 't':
return 'A';
default:
return base;
}
}
@ -407,7 +438,6 @@ public class BaseUtils {
return new String(simpleReverseComplement(bases.getBytes()));
}
/**
* Complement a String of bases. Preserves ambiguous bases.
*
@ -532,8 +562,8 @@ public class BaseUtils {
return BaseUtils.baseIndexToSimpleBase(getRandomBaseIndex(BaseUtils.simpleBaseToBaseIndex(excludeBase)));
}
/** Computes the smallest period >= minPeriod for the specified string. The period is defined as such p,
/**
* Computes the smallest period >= minPeriod for the specified string. The period is defined as such p,
* that for all i = 0... seq.length-1, seq[ i % p ] = seq[i] (or equivalently seq[i] = seq[i+p] for i=0...seq.length-1-p).
* The sequence does <i>not</i> have to contain whole number of periods. For instance, "ACACACAC" has a period
* of 2 (it has a period of 4 as well), and so does
@ -554,9 +584,7 @@ public class BaseUtils {
int offset = pos % period; // we are currenlty 'offset' bases into the putative repeat of period 'period'
// if our current hypothesis holds, base[pos] must be the same as base[offset]
if ( Character.toUpperCase( seq[pos] ) !=
Character.toUpperCase( seq[offset] )
) {
if (Character.toUpperCase(seq[pos]) != Character.toUpperCase(seq[offset])) {
// period we have been trying so far does not work.
// two possibilities:
@ -569,8 +597,10 @@ public class BaseUtils {
// we set period to pos (thus trying the hypothesis that bases from start up to the current one,
// non-inclusive are repeated hereafter), and decrement pos (this will re-test current base against the first base
// on the next loop re-entrance after pos is autoincremented)
if ( offset == 0 ) period = pos+1;
else period = pos-- ;
if (offset == 0)
period = pos + 1;
else
period = pos--;
}
}