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-deal with offsets that can be -1 

-added option to have "D"s inserted for deleted bases in pileup strings


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1635 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-16 16:44:57 +00:00
parent 01a9b1c63b
commit a7c306f757
2 changed files with 49 additions and 17 deletions
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36
java/src/org/broadinstitute/sting/utils/BasicPileup.java
View File

@ -37,13 +37,25 @@ abstract public class BasicPileup implements Pileup {
}
public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
return baseWithStrandPileupAsString( reads, offsets, false );
}
public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) {
StringBuilder bases = new StringBuilder();
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
char base = (char) read.getReadBases()[offset];
char base;
if ( offset == -1 ) {
if ( includeDeletions )
base = 'D';
else
continue;
} else {
base = (char) read.getReadBases()[offset];
}
base = Character.toUpperCase(base);
if (read.getReadNegativeStrandFlag()) {
@ -57,11 +69,20 @@ abstract public class BasicPileup implements Pileup {
}
public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets ) {
return basePileup( reads, offsets, false );
}
public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) {
ArrayList<Byte> bases = new ArrayList<Byte>(reads.size());
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
bases.add(read.getReadBases()[offset]);
if ( offset == -1 ) {
if ( includeDeletions )
bases.add((byte)'D');
} else {
bases.add(read.getReadBases()[offset]);
}
}
return bases;
}
@ -71,6 +92,9 @@ abstract public class BasicPileup implements Pileup {
for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i);
int offset = offsets.get(i);
// skip deletion sites
if ( offset == -1 )
continue;
byte qual = (byte)read.getBaseQualities()[offset];
quals.add(qual);
}
@ -117,7 +141,7 @@ abstract public class BasicPileup implements Pileup {
byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
byte base2;
if (compressedQuals != null && compressedQuals.length == read.getReadLength()) {
if (offset != -1 && compressedQuals != null && compressedQuals.length == read.getReadLength()) {
base2 = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(compressedQuals[offset]));
hasAtLeastOneSQField = true;
} else {
@ -168,7 +192,7 @@ abstract public class BasicPileup implements Pileup {
byte[] compressedQuals = (byte[]) read.getAttribute("SQ");
byte qual2;
if (compressedQuals != null) {
if (offset != -1 && compressedQuals != null) {
qual2 = QualityUtils.probToQual(QualityUtils.compressedQualityToProb(compressedQuals[offset]));
hasAtLeastOneSQField = true;
} else {
@ -201,6 +225,8 @@ abstract public class BasicPileup implements Pileup {
String bases = read.getReadString();
int offset = offsets.get(readIndex);
if ( offset == -1 )
continue;
int bestBaseIndex = BaseUtils.simpleBaseToBaseIndex(bases.charAt(offset));
@ -261,7 +287,7 @@ abstract public class BasicPileup implements Pileup {
{
SAMRecord read = reads.get(i);
Cigar cigar = read.getCigar();
int offset = offsets.get(i);
int offset = offsets.get(i);
String cigar_string = read.getCigarString();
if (! (cigar_string.contains("I") || cigar_string.contains("D"))) { indels[i] = "null"; continue; }

30
java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
View File

@ -17,6 +17,7 @@ public class ReadBackedPileup extends BasicPileup {
char ref;
List<SAMRecord> reads;
List<Integer> offsets;
boolean includeDeletions = false;
public ReadBackedPileup(char ref, AlignmentContext context ) {
this(context.getLocation(), ref, context.getReads(), context.getOffsets());
@ -37,6 +38,8 @@ public class ReadBackedPileup extends BasicPileup {
public List<SAMRecord> getReads() { return reads; }
public List<Integer> getOffsets() { return offsets; }
public void includeDeletionsInPileupString() { includeDeletions = true; }
public GenomeLoc getLocation() {
return loc;
}
@ -81,18 +84,21 @@ public class ReadBackedPileup extends BasicPileup {
public String getBasePileupAsCountsString() {
String bases = basePileupAsString(reads, offsets);
int[] counts = new int[4];
for (int i = 0; i < reads.size(); i++)
{
char base = Character.toUpperCase((char)(reads.get(i).getReadBases()[offsets.get(i)]));
if (BaseUtils.simpleBaseToBaseIndex(base) == -1) { continue; }
counts[BaseUtils.simpleBaseToBaseIndex(base)]++;
}
return String.format("A[%d] C[%d] G[%d] T[%d]",
counts[0],
counts[1],
counts[2],
counts[3]);
int[] counts = new int[4];
for (int i = 0; i < reads.size(); i++)
{
// skip deletion sites
if ( offsets.get(i) == -1 )
continue;
char base = Character.toUpperCase((char)(reads.get(i).getReadBases()[offsets.get(i)]));
if (BaseUtils.simpleBaseToBaseIndex(base) == -1) { continue; }
counts[BaseUtils.simpleBaseToBaseIndex(base)]++;
}
return String.format("A[%d] C[%d] G[%d] T[%d]",
counts[0],
counts[1],
counts[2],
counts[3]);
}
public String getProbDistPileup() {