zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Reformatting 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1778 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-07 20:03:34 +00:00
parent 203c626fc2
commit f9a1598d75
1 changed files with 25 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

50
java/src/org/broadinstitute/sting/utils/BasicPileup.java
View File

@ -21,7 +21,7 @@ abstract public class BasicPileup implements Pileup {
protected boolean includeDeletions = false; protected boolean includeDeletions = false;
public void setIncludeDeletionsInPileupString(boolean value) { public void setIncludeDeletionsInPileupString(boolean value) {
includeDeletions = value; includeDeletions = value;
} }
public String getPileupString() public String getPileupString()
@ -38,7 +38,7 @@ abstract public class BasicPileup implements Pileup {
} }
public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) { public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
return basePileupAsString( reads, offsets, false ); return basePileupAsString( reads, offsets, false );
} }
public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) { public static String basePileupAsString( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) {
@ -50,7 +50,7 @@ abstract public class BasicPileup implements Pileup {
} }
public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) { public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets ) {
return baseWithStrandPileupAsString( reads, offsets, false ); return baseWithStrandPileupAsString( reads, offsets, false );
} }
public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) { public static String baseWithStrandPileupAsString( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) {
@ -60,15 +60,15 @@ abstract public class BasicPileup implements Pileup {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
int offset = offsets.get(i); int offset = offsets.get(i);
char base; char base;
if ( offset == -1 ) { if ( offset == -1 ) {
if ( includeDeletions ) if ( includeDeletions )
base = DELETION_CHAR; base = DELETION_CHAR;
else else
continue; continue;
} else { } else {
base = (char) read.getReadBases()[offset]; base = (char) read.getReadBases()[offset];
} }
base = Character.toUpperCase(base); base = Character.toUpperCase(base);
if (read.getReadNegativeStrandFlag()) { if (read.getReadNegativeStrandFlag()) {
@ -82,7 +82,7 @@ abstract public class BasicPileup implements Pileup {
} }
public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets ) { public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets ) {
return basePileup( reads, offsets, false ); return basePileup( reads, offsets, false );
} }
public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) { public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets, boolean includeDeletions ) {
@ -90,24 +90,24 @@ abstract public class BasicPileup implements Pileup {
for ( int i = 0; i < reads.size(); i++ ) { for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
int offset = offsets.get(i); int offset = offsets.get(i);
if ( offset == -1 ) { if ( offset == -1 ) {
if ( includeDeletions ) if ( includeDeletions )
bases.add((byte)DELETION_CHAR); bases.add((byte)DELETION_CHAR);
} else { } else {
bases.add(read.getReadBases()[offset]); bases.add(read.getReadBases()[offset]);
} }
} }
return bases; return bases;
} }
public static ArrayList<Byte> qualPileup( List<SAMRecord> reads, List<Integer> offsets ) { public static ArrayList<Byte> qualPileup( List<SAMRecord> reads, List<Integer> offsets ) {
ArrayList<Byte> quals = new ArrayList<Byte>(reads.size()); ArrayList<Byte> quals = new ArrayList<Byte>(reads.size());
for ( int i = 0; i < reads.size(); i++ ) { for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
int offset = offsets.get(i); int offset = offsets.get(i);
// skip deletion sites // skip deletion sites
if ( offset == -1 ) if ( offset == -1 )
continue; continue;
byte qual = (byte)read.getBaseQualities()[offset]; byte qual = (byte)read.getBaseQualities()[offset];
quals.add(qual); quals.add(qual);
} }
@ -238,8 +238,8 @@ abstract public class BasicPileup implements Pileup {
String bases = read.getReadString(); String bases = read.getReadString();
int offset = offsets.get(readIndex); int offset = offsets.get(readIndex);
if ( offset == -1 ) if ( offset == -1 )
continue; continue;
int bestBaseIndex = BaseUtils.simpleBaseToBaseIndex(bases.charAt(offset)); int bestBaseIndex = BaseUtils.simpleBaseToBaseIndex(bases.charAt(offset));