Refactoring. Push the revisions to the common aligner interface down into
the aligner base classes. Hack the managed implementation to support the new interface. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna
parent
d84444200b
commit
4fbb6d05d0
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@ -17,21 +17,21 @@ static void set_int_configuration_param(JNIEnv* env, jobject configuration, cons
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static void set_float_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, float_setter setter);
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static void throw_config_value_exception(JNIEnv* env, const char* field_name, const char* message);
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JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create(JNIEnv* env, jobject instance, jobject configuration)
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JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create(JNIEnv* env, jobject instance, jobject bwtFiles, jobject configuration)
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{
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jstring java_ann = get_configuration_string(env,configuration,"annFileName");
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jstring java_ann = get_configuration_string(env,bwtFiles,"annFileName");
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if(env->ExceptionCheck()) return 0L;
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jstring java_amb = get_configuration_string(env,configuration,"ambFileName");
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jstring java_amb = get_configuration_string(env,bwtFiles,"ambFileName");
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if(env->ExceptionCheck()) return 0L;
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jstring java_pac = get_configuration_string(env,configuration,"pacFileName");
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jstring java_pac = get_configuration_string(env,bwtFiles,"pacFileName");
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if(env->ExceptionCheck()) return 0L;
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jstring java_forward_bwt = get_configuration_string(env,configuration,"forwardBWTFileName");
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jstring java_forward_bwt = get_configuration_string(env,bwtFiles,"forwardBWTFileName");
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if(env->ExceptionCheck()) return 0L;
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jstring java_forward_sa = get_configuration_string(env,configuration,"forwardSAFileName");
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jstring java_forward_sa = get_configuration_string(env,bwtFiles,"forwardSAFileName");
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if(env->ExceptionCheck()) return 0L;
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jstring java_reverse_bwt = get_configuration_string(env,configuration,"reverseBWTFileName");
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jstring java_reverse_bwt = get_configuration_string(env,bwtFiles,"reverseBWTFileName");
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if(env->ExceptionCheck()) return 0L;
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jstring java_reverse_sa = get_configuration_string(env,configuration,"reverseSAFileName");
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jstring java_reverse_sa = get_configuration_string(env,bwtFiles,"reverseSAFileName");
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if(env->ExceptionCheck()) return 0L;
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const char* ann_filename = env->GetStringUTFChars(java_ann,JNI_FALSE);
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@ -57,20 +57,8 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligne
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reverse_bwt_filename,
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reverse_sa_filename);
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set_float_configuration_param(env, configuration, "maximumEditDistance", bwa, &BWA::set_max_edit_distance);
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if(env->ExceptionCheck()) return 0L;
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set_int_configuration_param(env, configuration, "maximumGapOpens", bwa, &BWA::set_max_gap_opens);
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if(env->ExceptionCheck()) return 0L;
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set_int_configuration_param(env, configuration, "maximumGapExtensions", bwa, &BWA::set_max_gap_extensions);
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if(env->ExceptionCheck()) return 0L;
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set_int_configuration_param(env, configuration, "disallowIndelWithinRange", bwa, &BWA::set_disallow_indel_within_range);
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if(env->ExceptionCheck()) return 0L;
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set_int_configuration_param(env, configuration, "mismatchPenalty", bwa, &BWA::set_mismatch_penalty);
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if(env->ExceptionCheck()) return 0L;
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set_int_configuration_param(env, configuration, "gapOpenPenalty", bwa, &BWA::set_gap_open_penalty);
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if(env->ExceptionCheck()) return 0L;
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set_int_configuration_param(env, configuration, "gapExtensionPenalty", bwa, &BWA::set_gap_extension_penalty);
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if(env->ExceptionCheck()) return 0L;
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Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration(env,instance,(jlong)bwa,configuration);
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if(env->ExceptionCheck()) return 0L;
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env->ReleaseStringUTFChars(java_ann,ann_filename);
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if(env->ExceptionCheck()) return 0L;
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@ -96,6 +84,24 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
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delete bwa;
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}
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration(JNIEnv *env, jobject instance, jlong java_bwa, jobject configuration) {
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BWA* bwa = (BWA*)java_bwa;
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set_float_configuration_param(env, configuration, "maximumEditDistance", bwa, &BWA::set_max_edit_distance);
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if(env->ExceptionCheck()) return;
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set_int_configuration_param(env, configuration, "maximumGapOpens", bwa, &BWA::set_max_gap_opens);
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if(env->ExceptionCheck()) return;
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set_int_configuration_param(env, configuration, "maximumGapExtensions", bwa, &BWA::set_max_gap_extensions);
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if(env->ExceptionCheck()) return;
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set_int_configuration_param(env, configuration, "disallowIndelWithinRange", bwa, &BWA::set_disallow_indel_within_range);
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if(env->ExceptionCheck()) return;
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set_int_configuration_param(env, configuration, "mismatchPenalty", bwa, &BWA::set_mismatch_penalty);
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if(env->ExceptionCheck()) return;
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set_int_configuration_param(env, configuration, "gapOpenPenalty", bwa, &BWA::set_gap_open_penalty);
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if(env->ExceptionCheck()) return;
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set_int_configuration_param(env, configuration, "gapExtensionPenalty", bwa, &BWA::set_gap_extension_penalty);
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if(env->ExceptionCheck()) return;
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}
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JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getPaths(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases)
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{
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BWA* bwa = (BWA*)java_bwa;
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@ -10,10 +10,18 @@ extern "C" {
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/*
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* Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner
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* Method: create
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* Signature: (Lorg/broadinstitute/sting/alignment/bwa/c/BWACConfiguration;)J
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* Signature: (Lorg/broadinstitute/sting/alignment/bwa/BWTFiles;Lorg/broadinstitute/sting/alignment/bwa/BWAConfiguration;)J
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*/
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JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create
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(JNIEnv *, jobject, jobject);
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(JNIEnv *, jobject, jobject, jobject);
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/*
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* Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner
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* Method: updateConfiguration
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* Signature: (JLorg/broadinstitute/sting/alignment/bwa/BWAConfiguration;)V
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*/
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration
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(JNIEnv *, jobject, jlong, jobject);
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/*
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* Class: org_broadinstitute_sting_alignment_bwa_c_BWACAligner
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@ -1,8 +1,10 @@
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package org.broadinstitute.sting.alignment;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import java.util.List;
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import java.util.Iterator;
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/**
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* Create perfect alignments from the read to the genome represented by the given BWT / suffix array.
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@ -11,11 +13,40 @@ import java.util.List;
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* @version 0.1
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*/
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public interface Aligner {
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/**
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* Close this instance of the BWA pointer and delete its resources.
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*/
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public void close();
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/**
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* Allow the aligner to choose one alignment randomly from the pile of best alignments.
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* @param bases Bases to align.
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* @return An align
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*/
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public Alignment getBestAlignment(final byte[] bases);
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/**
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* Align the read to the reference.
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* @param read Read to align.
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* @param header Optional header to drop in place.
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* @return A list of the alignments.
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*/
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public List<Alignment> align(SAMRecord read);
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public SAMRecord align(final SAMRecord read, final SAMFileHeader header);
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/**
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* Get a iterator of alignments, batched by mapping quality.
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* @param bases List of bases.
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* @return Iterator to alignments.
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*/
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public Iterator<Alignment[]> getAllAlignments(final byte[] bases);
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/**
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* Get a iterator of aligned reads, batched by mapping quality.
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* @param read Read to align.
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* @param newHeader Optional new header to use when aligning the read. If present, it must be null.
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* @return Iterator to alignments.
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*/
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public Iterator<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader);
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}
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@ -1,8 +1,8 @@
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package org.broadinstitute.sting.alignment;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarOperator;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.BaseUtils;
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/**
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* Represents an alignment of a read to a site in the reference genome.
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@ -138,6 +138,13 @@ public class Alignment {
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* @param mappingQuality How good does BWA think this mapping is?
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* @param cigarOperators The ordered operators in the cigar string.
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* @param cigarLengths The lengths to which each operator applies.
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* @param editDistance The edit distance (cumulative) of the read.
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* @param mismatchingPositions String representation of which bases in the read mismatch.
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* @param numMismatches Number of total mismatches in the read.
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* @param numGapOpens Number of gap opens in the read.
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* @param numGapExtensions Number of gap extensions in the read.
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* @param bestCount Number of best alignments in the read.
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* @param secondBestCount Number of second best alignments in the read.
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*/
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public Alignment(int contigIndex,
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int alignmentStart,
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@ -166,4 +173,42 @@ public class Alignment {
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this.bestCount = bestCount;
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this.secondBestCount = secondBestCount;
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}
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/**
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* Creates a read directly from an alignment.
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* @param alignment The alignment to convert to a read.
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* @param unmappedRead Source of the unmapped read. Should have bases, quality scores, and flags.
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* @param newSAMHeader The new SAM header to use in creating this read. Can be null, but if so, the sequence
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* dictionary in the
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* @return A mapped alignment.
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*/
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public static SAMRecord convertToRead(Alignment alignment, SAMRecord unmappedRead, SAMFileHeader newSAMHeader) {
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SAMRecord read;
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try {
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read = (SAMRecord)unmappedRead.clone();
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}
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catch(CloneNotSupportedException ex) {
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throw new StingException("Unable to create aligned read from template.");
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}
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if(newSAMHeader != null)
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read.setHeader(newSAMHeader);
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if(alignment != null) {
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read.setReadUmappedFlag(false);
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read.setReferenceIndex(alignment.getContigIndex());
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read.setAlignmentStart((int)alignment.getAlignmentStart());
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read.setReadNegativeStrandFlag(alignment.isNegativeStrand());
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read.setMappingQuality(alignment.getMappingQuality());
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read.setCigar(alignment.getCigar());
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if(alignment.isNegativeStrand()) {
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read.setReadBases(BaseUtils.reverse(read.getReadBases()));
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read.setBaseQualities(BaseUtils.reverse(read.getBaseQualities()));
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}
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read.setAttribute("NM",alignment.getEditDistance());
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read.setAttribute("MD",alignment.getMismatchingPositions());
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}
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return read;
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}
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}
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@ -5,15 +5,11 @@ import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.cmdLine.Argument;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
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import org.broadinstitute.sting.alignment.bwa.c.BWAPath;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWTFiles;
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import net.sf.samtools.SAMRecord;
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import java.util.Iterator;
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import java.util.SortedMap;
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import java.util.TreeMap;
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import java.io.PrintWriter;
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import java.io.FileNotFoundException;
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/**
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* Validates alignments against existing reads.
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@ -43,8 +39,9 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
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*/
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@Override
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public void initialize() {
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BWACConfiguration configuration = new BWACConfiguration(prefix);
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aligner = new BWACAligner(configuration);
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BWTFiles bwtFiles = new BWTFiles(prefix);
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BWAConfiguration configuration = new BWAConfiguration();
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aligner = new BWACAligner(bwtFiles,configuration);
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}
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/** Must return true for reads that need to be processed. Reads, for which this method return false will
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@ -5,7 +5,8 @@ import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.WalkerName;
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import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
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import org.broadinstitute.sting.alignment.bwa.c.BWACConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
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import org.broadinstitute.sting.alignment.bwa.BWTFiles;
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import net.sf.samtools.*;
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import net.sf.picard.reference.ReferenceSequenceFileFactory;
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@ -36,6 +37,11 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
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*/
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private SAMFileWriter outputBam = null;
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/**
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* New header to use, if desired.
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*/
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private SAMFileHeader header = null;
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/** Must return true for reads that need to be processed. Reads, for which this method return false will
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* be skipped by the engine and never passed to the walker.
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*/
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@ -49,17 +55,21 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
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*/
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@Override
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public void initialize() {
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BWACConfiguration configuration = new BWACConfiguration(prefix);
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aligner = new BWACAligner(configuration);
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BWTFiles bwtFiles = new BWTFiles(prefix);
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BWAConfiguration configuration = new BWAConfiguration();
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aligner = new BWACAligner(bwtFiles,configuration);
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// HACK: If the sequence dictionary in the existing header is null, stuff the contents of the current reference
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// into it, so that the sequence has something to which to back-align.
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SAMFileHeader header = getToolkit().getSAMFileHeader();
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if(header.getSequenceDictionary().isEmpty()) {
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SAMFileHeader originalHeader = getToolkit().getSAMFileHeader();
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if(originalHeader.getSequenceDictionary().isEmpty()) {
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header = originalHeader.clone();
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SAMSequenceDictionary referenceDictionary =
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ReferenceSequenceFileFactory.getReferenceSequenceFile(getToolkit().getArguments().referenceFile).getSequenceDictionary();
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header.setSequenceDictionary(referenceDictionary);
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}
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else
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header = originalHeader;
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if ( outputBamFile != null ) {
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// Stuff the header from the fasta into that of the sequence dictionary.
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@ -75,7 +85,7 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
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*/
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@Override
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public Integer map(char[] ref, SAMRecord read) {
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SAMRecord alignedRead = aligner.align(read);
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SAMRecord alignedRead = aligner.align(read,header);
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if (outputBam != null) {
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outputBam.addAlignment(alignedRead);
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} else {
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@ -0,0 +1,31 @@
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package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.alignment.Aligner;
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import org.broadinstitute.sting.alignment.Alignment;
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import net.sf.samtools.SAMRecord;
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import net.sf.samtools.SAMFileHeader;
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import java.util.Iterator;
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/**
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* Align reads using BWA.
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*
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* @author mhanna
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* @version 0.1
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*/
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public abstract class BWAAligner implements Aligner {
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/**
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* Create a new BWAAligner. Purpose of this call is to ensure that all BWA constructors accept the correct
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* parameters.
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* @param bwtFiles The many files representing BWTs persisted to disk.
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* @param configuration Configuration parameters for the alignment.
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*/
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public BWAAligner(BWTFiles bwtFiles, BWAConfiguration configuration) { }
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/**
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* Update the configuration passed to the BWA aligner.
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* @param configuration New configuration to set.
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*/
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public abstract void updateConfiguration(BWAConfiguration configuration);
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}
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@ -0,0 +1,46 @@
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package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.utils.StingException;
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/**
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* Configuration for the BWA/C aligner.
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*
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* @author mhanna
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* @version 0.1
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*/
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public class BWAConfiguration {
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/**
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* The maximum edit distance used by BWA.
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*/
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public Float maximumEditDistance = null;
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/**
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* How many gap opens are acceptable within this alignment?
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*/
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public Integer maximumGapOpens = null;
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/**
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* How many gap extensions are acceptable within this alignment?
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*/
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public Integer maximumGapExtensions = null;
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/**
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* Do we disallow indels within a certain range from the start / end?
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*/
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public Integer disallowIndelWithinRange = null;
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/**
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* What is the scoring penalty for a mismatch?
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*/
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public Integer mismatchPenalty = null;
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/**
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* What is the scoring penalty for a gap open?
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*/
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public Integer gapOpenPenalty = null;
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/**
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* What is the scoring penalty for a gap extension?
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*/
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public Integer gapExtensionPenalty = null;
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}
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@ -0,0 +1,62 @@
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package org.broadinstitute.sting.alignment.bwa;
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import org.broadinstitute.sting.utils.StingException;
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/**
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* Support files for BWT.
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*
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* @author mhanna
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* @version 0.1
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*/
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||||
public class BWTFiles {
|
||||
/**
|
||||
* ANN (?) file name.
|
||||
*/
|
||||
public final String annFileName;
|
||||
|
||||
/**
|
||||
* AMB (?) file name.
|
||||
*/
|
||||
public final String ambFileName;
|
||||
|
||||
/**
|
||||
* Packed reference sequence file.
|
||||
*/
|
||||
public final String pacFileName;
|
||||
|
||||
/**
|
||||
* Forward BWT file.
|
||||
*/
|
||||
public final String forwardBWTFileName;
|
||||
|
||||
/**
|
||||
* Forward suffix array file.
|
||||
*/
|
||||
public final String forwardSAFileName;
|
||||
|
||||
/**
|
||||
* Reverse BWT file.
|
||||
*/
|
||||
public final String reverseBWTFileName;
|
||||
|
||||
/**
|
||||
* Reverse suffix array file.
|
||||
*/
|
||||
public final String reverseSAFileName;
|
||||
|
||||
/**
|
||||
* Create a new BWA configuration file using the given prefix.
|
||||
* @param prefix Prefix to use when creating the configuration. Must not be null.
|
||||
*/
|
||||
public BWTFiles(String prefix) {
|
||||
if(prefix == null)
|
||||
throw new StingException("Prefix must not be null.");
|
||||
annFileName = prefix + ".ann";
|
||||
ambFileName = prefix + ".amb";
|
||||
pacFileName = prefix + ".pac";
|
||||
forwardBWTFileName = prefix + ".bwt";
|
||||
forwardSAFileName = prefix + ".sa";
|
||||
reverseBWTFileName = prefix + ".rbwt";
|
||||
reverseSAFileName = prefix + ".rsa";
|
||||
}
|
||||
}
|
||||
|
|
@ -1,9 +1,13 @@
|
|||
package org.broadinstitute.sting.alignment.bwa.c;
|
||||
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import net.sf.samtools.SAMFileHeader;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
import org.broadinstitute.sting.utils.BaseUtils;
|
||||
import org.broadinstitute.sting.alignment.Alignment;
|
||||
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
|
||||
import org.broadinstitute.sting.alignment.bwa.BWTFiles;
|
||||
import org.broadinstitute.sting.alignment.bwa.BWAAligner;
|
||||
|
||||
import java.util.*;
|
||||
import java.io.File;
|
||||
|
|
@ -14,7 +18,7 @@ import java.io.File;
|
|||
* @author mhanna
|
||||
* @version 0.1
|
||||
*/
|
||||
public class BWACAligner {
|
||||
public class BWACAligner extends BWAAligner {
|
||||
static {
|
||||
System.loadLibrary("bwa");
|
||||
}
|
||||
|
|
@ -24,25 +28,37 @@ public class BWACAligner {
|
|||
*/
|
||||
private long thunkPointer = 0;
|
||||
|
||||
public BWACAligner(BWACConfiguration configuration) {
|
||||
public BWACAligner(BWTFiles bwtFiles, BWAConfiguration configuration) {
|
||||
super(bwtFiles,configuration);
|
||||
if(thunkPointer != 0)
|
||||
throw new StingException("BWA/C attempting to reinitialize.");
|
||||
|
||||
if(!new File(configuration.annFileName).exists()) throw new StingException("ANN file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(configuration.ambFileName).exists()) throw new StingException("AMB file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(configuration.pacFileName).exists()) throw new StingException("PAC file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(configuration.forwardBWTFileName).exists()) throw new StingException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(configuration.forwardSAFileName).exists()) throw new StingException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(configuration.reverseBWTFileName).exists()) throw new StingException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(configuration.reverseSAFileName).exists()) throw new StingException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.annFileName).exists()) throw new StingException("ANN file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.ambFileName).exists()) throw new StingException("AMB file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.pacFileName).exists()) throw new StingException("PAC file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.forwardBWTFileName).exists()) throw new StingException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.forwardSAFileName).exists()) throw new StingException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.reverseBWTFileName).exists()) throw new StingException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
if(!new File(bwtFiles.reverseSAFileName).exists()) throw new StingException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it.");
|
||||
|
||||
thunkPointer = create(configuration);
|
||||
thunkPointer = create(bwtFiles,configuration);
|
||||
}
|
||||
|
||||
/**
|
||||
* Update the configuration passed to the BWA aligner.
|
||||
* @param configuration New configuration to set.
|
||||
*/
|
||||
@Override
|
||||
public void updateConfiguration(BWAConfiguration configuration) {
|
||||
if(thunkPointer != 0)
|
||||
throw new StingException("BWA/C: attempting to update configuration of uninitialized aligner.");
|
||||
updateConfiguration(thunkPointer,configuration);
|
||||
}
|
||||
|
||||
/**
|
||||
* Close this instance of the BWA pointer and delete its resources.
|
||||
*/
|
||||
@Override
|
||||
public void close() {
|
||||
if(thunkPointer == 0)
|
||||
throw new StingException("BWA/C close attempted, but BWA/C is not properly initialized.");
|
||||
|
|
@ -54,6 +70,7 @@ public class BWACAligner {
|
|||
* @param bases Bases to align.
|
||||
* @return An align
|
||||
*/
|
||||
@Override
|
||||
public Alignment getBestAlignment(final byte[] bases) {
|
||||
if(thunkPointer == 0)
|
||||
throw new StingException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized.");
|
||||
|
|
@ -63,10 +80,12 @@ public class BWACAligner {
|
|||
/**
|
||||
* Get the best aligned read, chosen randomly from the pile of best alignments.
|
||||
* @param read Read to align.
|
||||
* @param newHeader New header to apply to this SAM file. Can be null, but if so, read header must be valid.
|
||||
* @return Read with injected alignment data.
|
||||
*/
|
||||
public SAMRecord align(final SAMRecord read) {
|
||||
return convertAlignmentToRead(read,getBestAlignment(read.getReadBases()));
|
||||
@Override
|
||||
public SAMRecord align(final SAMRecord read, final SAMFileHeader newHeader) {
|
||||
return Alignment.convertToRead(getBestAlignment(read.getReadBases()),read,newHeader);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -74,6 +93,7 @@ public class BWACAligner {
|
|||
* @param bases List of bases.
|
||||
* @return Iterator to alignments.
|
||||
*/
|
||||
@Override
|
||||
public Iterator<Alignment[]> getAllAlignments(final byte[] bases) {
|
||||
final BWAPath[] paths = getPaths(bases);
|
||||
return new Iterator<Alignment[]>() {
|
||||
|
|
@ -111,9 +131,11 @@ public class BWACAligner {
|
|||
/**
|
||||
* Get a iterator of aligned reads, batched by mapping quality.
|
||||
* @param read Read to align.
|
||||
* @param newHeader Optional new header to use when aligning the read. If present, it must be null.
|
||||
* @return Iterator to alignments.
|
||||
*/
|
||||
public Iterator<SAMRecord[]> alignAll(final SAMRecord read) {
|
||||
@Override
|
||||
public Iterator<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) {
|
||||
final Iterator<Alignment[]> alignments = getAllAlignments(read.getReadBases());
|
||||
return new Iterator<SAMRecord[]>() {
|
||||
/**
|
||||
|
|
@ -130,7 +152,7 @@ public class BWACAligner {
|
|||
Alignment[] alignmentsOfQuality = alignments.next();
|
||||
SAMRecord[] reads = new SAMRecord[alignmentsOfQuality.length];
|
||||
for(int i = 0; i < alignmentsOfQuality.length; i++) {
|
||||
reads[i] = convertAlignmentToRead(read,alignmentsOfQuality[i]);
|
||||
reads[i] = Alignment.convertToRead(alignmentsOfQuality[i],read,newHeader);
|
||||
}
|
||||
return reads;
|
||||
}
|
||||
|
|
@ -142,37 +164,6 @@ public class BWACAligner {
|
|||
};
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates a read directly from an alignment.
|
||||
* @param unmappedRead Source of the unmapped read. Should have bases, quality scores, and flags.
|
||||
* @param alignment The target alignment for this read. If alignment is null, assume the read is unmappe.d
|
||||
* @return A mapped alignment.
|
||||
*/
|
||||
public SAMRecord convertAlignmentToRead(SAMRecord unmappedRead, Alignment alignment) {
|
||||
SAMRecord read = null;
|
||||
try {
|
||||
read = (SAMRecord)unmappedRead.clone();
|
||||
if(alignment != null) {
|
||||
read.setReadUmappedFlag(false);
|
||||
read.setReferenceIndex(alignment.getContigIndex());
|
||||
read.setAlignmentStart((int)alignment.getAlignmentStart());
|
||||
read.setReadNegativeStrandFlag(alignment.isNegativeStrand());
|
||||
read.setMappingQuality(alignment.getMappingQuality());
|
||||
read.setCigar(alignment.getCigar());
|
||||
if(alignment.isNegativeStrand()) {
|
||||
read.setReadBases(BaseUtils.reverse(read.getReadBases()));
|
||||
read.setBaseQualities(BaseUtils.reverse(read.getBaseQualities()));
|
||||
}
|
||||
read.setAttribute("NM",alignment.getEditDistance());
|
||||
read.setAttribute("MD",alignment.getMismatchingPositions());
|
||||
}
|
||||
}
|
||||
catch(CloneNotSupportedException ex) {
|
||||
throw new StingException("Unable to create aligned read from template.");
|
||||
}
|
||||
return read;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the paths associated with the given base string.
|
||||
* @param bases List of bases.
|
||||
|
|
@ -181,16 +172,23 @@ public class BWACAligner {
|
|||
public BWAPath[] getPaths(byte[] bases) {
|
||||
if(thunkPointer == 0)
|
||||
throw new StingException("BWA/C getPaths attempted, but BWA/C is not properly initialized.");
|
||||
BWAPath[] paths = getPaths(thunkPointer,bases);
|
||||
return paths;
|
||||
return getPaths(thunkPointer,bases);
|
||||
}
|
||||
|
||||
/**
|
||||
* Create a pointer to the BWA/C thunk.
|
||||
* @param files BWT source files.
|
||||
* @param configuration Configuration of the aligner.
|
||||
* @return Pointer to the BWA/C thunk.
|
||||
*/
|
||||
protected native long create(BWACConfiguration configuration);
|
||||
protected native long create(BWTFiles files, BWAConfiguration configuration);
|
||||
|
||||
/**
|
||||
* Update the configuration passed to the BWA aligner. For internal use only.
|
||||
* @param thunkPointer pointer to BWA object.
|
||||
* @param configuration New configuration to set.
|
||||
*/
|
||||
protected native void updateConfiguration(long thunkPointer, BWAConfiguration configuration);
|
||||
|
||||
/**
|
||||
* Destroy the BWA/C thunk.
|
||||
|
|
|
|||
|
|
@ -1,98 +0,0 @@
|
|||
package org.broadinstitute.sting.alignment.bwa.c;
|
||||
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
||||
/**
|
||||
* Configuration for the BWA/C aligner.
|
||||
*
|
||||
* @author mhanna
|
||||
* @version 0.1
|
||||
*/
|
||||
public class BWACConfiguration {
|
||||
/**
|
||||
* ANN (?) file name.
|
||||
*/
|
||||
public String annFileName = null;
|
||||
|
||||
/**
|
||||
* AMB (?) file name.
|
||||
*/
|
||||
public String ambFileName = null;
|
||||
|
||||
/**
|
||||
* Packed reference sequence file.
|
||||
*/
|
||||
public String pacFileName = null;
|
||||
|
||||
/**
|
||||
* Forward BWT file.
|
||||
*/
|
||||
public String forwardBWTFileName = null;
|
||||
|
||||
/**
|
||||
* Forward suffix array file.
|
||||
*/
|
||||
public String forwardSAFileName = null;
|
||||
|
||||
/**
|
||||
* Reverse BWT file.
|
||||
*/
|
||||
public String reverseBWTFileName = null;
|
||||
|
||||
/**
|
||||
* Reverse suffix array file.
|
||||
*/
|
||||
public String reverseSAFileName = null;
|
||||
|
||||
/**
|
||||
* The maximum edit distance used by BWA.
|
||||
*/
|
||||
public Float maximumEditDistance = null;
|
||||
|
||||
/**
|
||||
* How many gap opens are acceptable within this alignment?
|
||||
*/
|
||||
public Integer maximumGapOpens = null;
|
||||
|
||||
/**
|
||||
* How many gap extensions are acceptable within this alignment?
|
||||
*/
|
||||
public Integer maximumGapExtensions = null;
|
||||
|
||||
/**
|
||||
* Do we disallow indels within a certain range from the start / end?
|
||||
*/
|
||||
public Integer disallowIndelWithinRange = null;
|
||||
|
||||
/**
|
||||
* What is the scoring penalty for a mismatch?
|
||||
*/
|
||||
public Integer mismatchPenalty = null;
|
||||
|
||||
/**
|
||||
* What is the scoring penalty for a gap open?
|
||||
*/
|
||||
public Integer gapOpenPenalty = null;
|
||||
|
||||
/**
|
||||
* What is the scoring penalty for a gap extension?
|
||||
*/
|
||||
public Integer gapExtensionPenalty = null;
|
||||
|
||||
/**
|
||||
* Create a new BWA configuration file using the given prefix.
|
||||
* @param prefix Prefix to use when creating the configuration. Must not be null.
|
||||
*/
|
||||
public BWACConfiguration(String prefix) {
|
||||
if(prefix == null)
|
||||
throw new StingException("Prefix must not be null.");
|
||||
annFileName = prefix + ".ann";
|
||||
ambFileName = prefix + ".amb";
|
||||
pacFileName = prefix + ".pac";
|
||||
forwardBWTFileName = prefix + ".bwt";
|
||||
forwardSAFileName = prefix + ".sa";
|
||||
reverseBWTFileName = prefix + ".rbwt";
|
||||
reverseSAFileName = prefix + ".rsa";
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.java;
|
|||
|
||||
import org.broadinstitute.sting.alignment.Aligner;
|
||||
import org.broadinstitute.sting.alignment.Alignment;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.BWAAligner;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.BWAAlignment;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
|
@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
|
|||
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.util.List;
|
||||
import java.util.Iterator;
|
||||
|
||||
import net.sf.samtools.*;
|
||||
|
||||
|
|
@ -39,7 +39,7 @@ public class AlignerTestHarness {
|
|||
}
|
||||
|
||||
private static void align(File referenceFile, File bwtFile, File rbwtFile, File suffixArrayFile, File reverseSuffixArrayFile, File bamFile) throws FileNotFoundException {
|
||||
Aligner aligner = new BWAAligner(bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile);
|
||||
Aligner aligner = new BWAJavaAligner(bwtFile,rbwtFile,suffixArrayFile,reverseSuffixArrayFile);
|
||||
int count = 0;
|
||||
|
||||
SAMFileReader reader = new SAMFileReader(bamFile);
|
||||
|
|
@ -79,21 +79,24 @@ public class AlignerTestHarness {
|
|||
// Clear everything except flags pertaining to pairing and set 'unmapped' status to true.
|
||||
alignmentCleaned.setFlags(alignmentCleaned.getFlags() & 0x00A1 | 0x000C);
|
||||
|
||||
List<Alignment> alignments = aligner.align(alignmentCleaned);
|
||||
if(alignments.size() == 0 ) {
|
||||
Iterator<Alignment[]> alignments = aligner.getAllAlignments(alignmentCleaned.getReadBases());
|
||||
if(!alignments.hasNext() ) {
|
||||
//throw new StingException(String.format("Unable to align read %s to reference; count = %d",read.getReadName(),count));
|
||||
System.out.printf("Unable to align read %s to reference; count = %d%n",read.getReadName(),count);
|
||||
failures++;
|
||||
}
|
||||
|
||||
Alignment foundAlignment = null;
|
||||
for( Alignment alignment: alignments ) {
|
||||
if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
|
||||
continue;
|
||||
if( read.getAlignmentStart() != alignment.getAlignmentStart() )
|
||||
continue;
|
||||
while(alignments.hasNext()) {
|
||||
Alignment[] alignmentsOfQuality = alignments.next();
|
||||
for(Alignment alignment: alignmentsOfQuality) {
|
||||
if( read.getReadNegativeStrandFlag() != alignment.isNegativeStrand() )
|
||||
continue;
|
||||
if( read.getAlignmentStart() != alignment.getAlignmentStart() )
|
||||
continue;
|
||||
|
||||
foundAlignment = alignment;
|
||||
foundAlignment = alignment;
|
||||
}
|
||||
}
|
||||
|
||||
if( foundAlignment != null ) {
|
||||
|
|
@ -113,18 +116,22 @@ public class AlignerTestHarness {
|
|||
String expectedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),read.getAlignmentStart(),read.getAlignmentStart()+read.getReadLength()+numDeletions-1).getBases());
|
||||
System.out.printf("expected ref = %s%n", formatBasesBasedOnCigar(expectedRef,read.getCigar(),CigarOperator.INSERTION));
|
||||
|
||||
for( Alignment alignment: alignments ) {
|
||||
System.out.println();
|
||||
Iterator<Alignment[]> alignmentsToOutput = aligner.getAllAlignments(alignmentCleaned.getReadBases());
|
||||
while(alignmentsToOutput.hasNext()) {
|
||||
Alignment[] alignmentsOfQuality = alignments.next();
|
||||
for(Alignment alignment: alignmentsOfQuality) {
|
||||
System.out.println();
|
||||
|
||||
Cigar cigar = ((BWAAlignment)alignment).getCigar();
|
||||
Cigar cigar = ((BWAAlignment)alignment).getCigar();
|
||||
|
||||
System.out.printf("read = %s%n", formatBasesBasedOnCigar(read.getReadString(),cigar,CigarOperator.DELETION));
|
||||
System.out.printf("read = %s%n", formatBasesBasedOnCigar(read.getReadString(),cigar,CigarOperator.DELETION));
|
||||
|
||||
int deletionCount = ((BWAAlignment)alignment).getNumberOfBasesMatchingState(AlignmentState.DELETION);
|
||||
String alignedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignment.getAlignmentStart(),alignment.getAlignmentStart()+read.getReadLength()+deletionCount-1).getBases());
|
||||
System.out.printf("actual ref = %s, position = %d, negative strand = %b%n", formatBasesBasedOnCigar(alignedRef,cigar,CigarOperator.INSERTION),
|
||||
alignment.getAlignmentStart(),
|
||||
alignment.isNegativeStrand());
|
||||
int deletionCount = ((BWAAlignment)alignment).getNumberOfBasesMatchingState(AlignmentState.DELETION);
|
||||
String alignedRef = new String(reference.getSubsequenceAt(reference.getSequenceDictionary().getSequences().get(0).getSequenceName(),alignment.getAlignmentStart(),alignment.getAlignmentStart()+read.getReadLength()+deletionCount-1).getBases());
|
||||
System.out.printf("actual ref = %s, position = %d, negative strand = %b%n", formatBasesBasedOnCigar(alignedRef,cigar,CigarOperator.INSERTION),
|
||||
alignment.getAlignmentStart(),
|
||||
alignment.isNegativeStrand());
|
||||
}
|
||||
}
|
||||
|
||||
//throw new StingException(String.format("Read %s was placed at incorrect location; count = %d%n",read.getReadName(),count));
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
package org.broadinstitute.sting.alignment.bwa.java;
|
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|
||||
import org.broadinstitute.sting.alignment.Alignment;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.BWAAligner;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
|
||||
import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
|
||||
import org.broadinstitute.sting.utils.StingException;
|
||||
|
|
@ -28,7 +28,7 @@ public class BWAAlignment extends Alignment implements Cloneable {
|
|||
/**
|
||||
* The aligner performing the alignments.
|
||||
*/
|
||||
protected BWAAligner aligner;
|
||||
protected BWAJavaAligner aligner;
|
||||
|
||||
/**
|
||||
* The sequence of matches/mismatches/insertions/deletions.
|
||||
|
|
@ -136,7 +136,7 @@ public class BWAAlignment extends Alignment implements Cloneable {
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|||
* Create a new alignment with the given parent aligner.
|
||||
* @param aligner Aligner being used.
|
||||
*/
|
||||
public BWAAlignment( BWAAligner aligner ) {
|
||||
public BWAAlignment( BWAJavaAligner aligner ) {
|
||||
this.aligner = aligner;
|
||||
this.creationNumber = numCreated++;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ import java.io.File;
|
|||
import java.util.*;
|
||||
|
||||
import net.sf.samtools.SAMRecord;
|
||||
import net.sf.samtools.SAMFileHeader;
|
||||
|
||||
/**
|
||||
* Create imperfect alignments from the read to the genome represented by the given BWT / suffix array.
|
||||
|
|
@ -19,7 +20,7 @@ import net.sf.samtools.SAMRecord;
|
|||
* @author mhanna
|
||||
* @version 0.1
|
||||
*/
|
||||
public class BWAAligner implements Aligner {
|
||||
public class BWAJavaAligner implements Aligner {
|
||||
/**
|
||||
* BWT in the forward direction.
|
||||
*/
|
||||
|
|
@ -75,13 +76,49 @@ public class BWAAligner implements Aligner {
|
|||
*/
|
||||
public final int INDEL_END_SKIP = 5;
|
||||
|
||||
public BWAAligner( File forwardBWTFile, File reverseBWTFile, File forwardSuffixArrayFile, File reverseSuffixArrayFile ) {
|
||||
public BWAJavaAligner( File forwardBWTFile, File reverseBWTFile, File forwardSuffixArrayFile, File reverseSuffixArrayFile ) {
|
||||
forwardBWT = new BWTReader(forwardBWTFile).read();
|
||||
reverseBWT = new BWTReader(reverseBWTFile).read();
|
||||
forwardSuffixArray = new SuffixArrayReader(forwardSuffixArrayFile,forwardBWT).read();
|
||||
reverseSuffixArray = new SuffixArrayReader(reverseSuffixArrayFile,reverseBWT).read();
|
||||
}
|
||||
|
||||
/**
|
||||
* Close this instance of the BWA pointer and delete its resources.
|
||||
*/
|
||||
public void close() { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
|
||||
|
||||
/**
|
||||
* Allow the aligner to choose one alignment randomly from the pile of best alignments.
|
||||
* @param bases Bases to align.
|
||||
* @return An align
|
||||
*/
|
||||
public Alignment getBestAlignment(final byte[] bases) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
|
||||
|
||||
/**
|
||||
* Align the read to the reference.
|
||||
* @param read Read to align.
|
||||
* @param header Optional header to drop in place.
|
||||
* @return A list of the alignments.
|
||||
*/
|
||||
public SAMRecord align(final SAMRecord read, final SAMFileHeader header) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
|
||||
|
||||
/**
|
||||
* Get a iterator of alignments, batched by mapping quality.
|
||||
* @param bases List of bases.
|
||||
* @return Iterator to alignments.
|
||||
*/
|
||||
public Iterator<Alignment[]> getAllAlignments(final byte[] bases) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
|
||||
|
||||
/**
|
||||
* Get a iterator of aligned reads, batched by mapping quality.
|
||||
* @param read Read to align.
|
||||
* @param newHeader Optional new header to use when aligning the read. If present, it must be null.
|
||||
* @return Iterator to alignments.
|
||||
*/
|
||||
public Iterator<SAMRecord[]> alignAll(final SAMRecord read, final SAMFileHeader newHeader) { throw new UnsupportedOperationException("BWAJavaAligner does not yet support the standard Aligner interface."); }
|
||||
|
||||
|
||||
public List<Alignment> align( SAMRecord read ) {
|
||||
List<Alignment> successfulMatches = new ArrayList<Alignment>();
|
||||
|
||||
Loading…
Reference in New Issue