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Create artificial reads with "default" parameters 

* added functions to create synthetic reads for unit testing with reasonable default parameters
* added more functions to create synthetic reads based on cigar string + bases and quals.
This commit is contained in:
Mauricio Carneiro 2011-12-14 16:51:55 -05:00
parent c85100ce9c
commit 128bdf9c09
1 changed files with 42 additions and 0 deletions
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42
public/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
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@ -200,6 +200,48 @@ public class ArtificialSAMUtils {
return rec; return rec;
} }
/**
* Create an artificial read based on the parameters
*
* @param header the SAM header to associate the read with
* @param name the name of the read
* @param refIndex the reference index, i.e. what chromosome to associate it with
* @param alignmentStart where to start the alignment
* @param bases the sequence of the read
* @param qual the qualities of the read
* @param cigar the cigar string of the read
*
* @return the artificial read
*/
public static GATKSAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual, String cigar ) {
GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases, qual);
rec.setCigarString(cigar);
return rec;
}
/**
* Create an artificial read with the following default parameters :
* header:
* numberOfChromosomes = 1
* startingChromosome = 1
* chromosomeSize = 1000000
* read:
* name = "default_read"
* refIndex = 0
* alignmentStart = 1
*
* @param bases the sequence of the read
* @param qual the qualities of the read
* @param cigar the cigar string of the read
*
* @return the artificial read
*/
public static GATKSAMRecord createArtificialRead( byte[] bases, byte[] qual, String cigar ) {
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);
return ArtificialSAMUtils.createArtificialRead(header, "default_read", 0, 1, bases, qual, cigar);
}
public final static List<GATKSAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) { public final static List<GATKSAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
GATKSAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen); GATKSAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen);
GATKSAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen); GATKSAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen);