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Successfully writing .sa files. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1549 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-09-08 17:34:34 +00:00
parent 600c234643
commit f22f590192
2 changed files with 67 additions and 27 deletions
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52
java/src/org/broadinstitute/sting/bwa/CreateBWTFromReference.java
View File

@ -99,6 +99,13 @@ public class CreateBWTFromReference {
return compressedSuffixArray;
}
private int[] createInversedCompressedSuffixArray( int[] compressedSuffixArray ) {
int[] inverseCompressedSuffixArray = new int[compressedSuffixArray.length];
for( int i = 0; i < compressedSuffixArray.length; i++ )
inverseCompressedSuffixArray[compressedSuffixArray[i]] = i;
return inverseCompressedSuffixArray;
}
private byte[] createBWT( String sequence, int[] suffixArray ) {
byte[] bwt = new byte[suffixArray.length];
for( int i = 0; i < suffixArray.length; i++ ) {
@ -111,16 +118,19 @@ public class CreateBWTFromReference {
}
public static void main( String argv[] ) throws IOException {
if( argv.length != 2 ) {
System.out.println("USAGE: CreateBWTFromReference <input>.fasta <output>");
if( argv.length != 3 ) {
System.out.println("USAGE: CreateBWTFromReference <input>.fasta <output bwt> <output sa>");
return;
}
String inputFileName = argv[0];
File inputFile = new File(inputFileName);
String outputFileName = argv[1];
File outputFile = new File(outputFileName);
String bwtFileName = argv[1];
File bwtFile = new File(bwtFileName);
String saFileName = argv[2];
File saFile = new File(saFileName);
CreateBWTFromReference creator = new CreateBWTFromReference();
@ -144,6 +154,12 @@ public class CreateBWTFromReference {
reconstructedInverseSA = compressedSuffixArray[reconstructedInverseSA];
}
// Create the data structure for the inverse compressed suffix array and print diagnostics.
int[] inverseCompressedSuffixArray = creator.createInversedCompressedSuffixArray(compressedSuffixArray);
for( int i = 0; i < 8; i++ ) {
System.out.printf("inverseCompressedSuffixArray[%d] = %d%n", i, inverseCompressedSuffixArray[i]);
}
// Count the occurences of each given base.
int[] occurrences = creator.countOccurrences(sequence);
System.out.printf("Occurrences: a=%d, c=%d, g=%d, t=%d%n",occurrences[0],occurrences[1],occurrences[2],occurrences[3]);
@ -152,27 +168,39 @@ public class CreateBWTFromReference {
byte[] bwt = creator.createBWT(sequence, suffixArray);
String bwtAsString = new String(bwt);
System.out.printf("BWT:%n");
//System.out.printf("BWT:%n");
while( bwtAsString.length() > 0 ) {
int end = Math.min( 80, bwtAsString.length() );
//System.out.printf("%s%n", bwtAsString.substring(0,end));
bwtAsString = bwtAsString.substring(end);
}
OutputStream outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
OutputStream bwtOutputStream = new BufferedOutputStream(new FileOutputStream(bwtFile));
ByteBuffer buffer = ByteBuffer.allocate(4).order(ByteOrder.LITTLE_ENDIAN);
buffer.putInt(inverseSuffixArray[0]);
outputStream.write(buffer.array());
outputStream.flush();
bwtOutputStream.write(buffer.array());
bwtOutputStream.flush();
OccurrenceOutputStream occurrenceWriter = new OccurrenceOutputStream(outputStream);
PackedIntOutputStream occurrenceWriter = new PackedIntOutputStream(bwtOutputStream);
occurrenceWriter.write(occurrences);
occurrenceWriter.flush();
WordPackedOutputStream bwtOutputStream = new WordPackedOutputStream(outputStream,ByteOrder.LITTLE_ENDIAN);
bwtOutputStream.write(bwt);
bwtOutputStream.close();
WordPackedOutputStream sequenceOutputStream = new WordPackedOutputStream(bwtOutputStream,ByteOrder.LITTLE_ENDIAN);
sequenceOutputStream.write(bwt);
sequenceOutputStream.close();
OutputStream saOutputStream = new BufferedOutputStream(new FileOutputStream(saFile));
PackedIntOutputStream saIntWriter = new PackedIntOutputStream(saOutputStream);
// SA file format is 'primary' (= SA-1[0]?), occurrence array, interval, sequence length, SA[]
saIntWriter.write(inverseSuffixArray[0]);
saIntWriter.write(occurrences);
saIntWriter.write(1);
saIntWriter.write(suffixArray.length-1);
saIntWriter.write(suffixArray, 1, suffixArray.length-1);
saIntWriter.close();
}
/**

42
java/src/org/broadinstitute/sting/bwa/OccurrenceOutputStream.java → java/src/org/broadinstitute/sting/bwa/PackedIntOutputStream.java
View File

@ -37,7 +37,7 @@ import java.nio.ByteOrder;
* @author mhanna
* @version 0.1
*/
public class OccurrenceOutputStream {
public class PackedIntOutputStream {
/**
* How many bytes does it take to hold an integer in Java?
*/
@ -49,35 +49,47 @@ public class OccurrenceOutputStream {
private final OutputStream targetOutputStream;
/**
* Create a new OccurrenceArrayOutputStream, writing to the given target file.
* Create a new PackedIntOutputStream, writing to the given target file.
* @param outputFile target output file.
* @throws IOException if an I/O error occurs.
*/
public OccurrenceOutputStream( File outputFile ) throws IOException {
public PackedIntOutputStream( File outputFile ) throws IOException {
this(new FileOutputStream(outputFile));
}
/**
* Write occurrence array to the given OutputStream.
* @param outputStream Output stream to which to write packed bases.
* Write packed ints to the given OutputStream.
* @param outputStream Output stream to which to write packed ints.
* @throws IOException if an I/O error occurs.
*/
public OccurrenceOutputStream( OutputStream outputStream ) throws IOException {
public PackedIntOutputStream( OutputStream outputStream ) throws IOException {
this.targetOutputStream = outputStream;
}
/**
* Write the cumulative occurrences to the output stream.
* @param occurrences occurrences to write. occurrences.length must match alphabet size.
* Write the data to the output stream.
* @param datum datum to write.
* @throws IOException if an I/O error occurs.
*/
public void write( int[] occurrences ) throws IOException {
if( occurrences.length > BytePackedOutputStream.ALPHABET_SIZE )
throw new StingException("Wrong number of occurrence data points; expected " + BytePackedOutputStream.ALPHABET_SIZE);
ByteBuffer buffer = ByteBuffer.allocate(INT_SIZE_IN_BYTES*occurrences.length).order(ByteOrder.LITTLE_ENDIAN);
for(int occurrence: occurrences)
buffer.putInt(occurrence);
targetOutputStream.write(buffer.array());
public void write( int datum ) throws IOException {
ByteBuffer buffer = ByteBuffer.allocate(INT_SIZE_IN_BYTES).order(ByteOrder.LITTLE_ENDIAN);
buffer.putInt(datum);
targetOutputStream.write(buffer.array());
}
/**
* Write the data to the output stream.
* @param data data to write. occurrences.length must match alphabet size.
* @throws IOException if an I/O error occurs.
*/
public void write( int[] data ) throws IOException {
for(int datum: data)
write(datum);
}
public void write( int[] data, int offset, int length ) throws IOException {
for( int i = offset; i < offset+length; i++ )
write(data[i]);
}
/**