Support MAF record writing

src/main/java/org/cbioportal/file/export/ClinicalAttributeDataWriter.java

@@ -6,12 +6,11 @@
 import java.io.IOException;
 import java.io.Writer;
 import java.util.*;
-import java.util.stream.Collectors;
-import java.util.stream.StreamSupport;
+
+import static org.cbioportal.file.export.TSVUtil.composeRow;
 
 public class ClinicalAttributeDataWriter {
 
-    public static final String TAB = "\t";
     private final Writer writer;
 
     /**
@@ -55,8 +54,5 @@ private void writeCommentsRow(Iterable<String> row) {
         }
     }
 
-    private static String composeRow(Iterable<String> row) {
-        return StreamSupport.stream(row.spliterator(), false)
-            .map(s -> s.replace(TAB, "\\t")).collect(Collectors.joining(TAB)) + "\n";
-    }
+
 }

src/main/java/org/cbioportal/file/export/MafRecordWriter.java

@@ -0,0 +1,79 @@
+package org.cbioportal.file.export;
+
+import org.cbioportal.file.model.MafRecord;
+
+import java.io.IOException;
+import java.io.Writer;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+
+import static org.cbioportal.file.export.TSVUtil.composeRow;
+
+/**
+ * Writes MAF records to a writer
+ */
+public class MafRecordWriter {
+    private final Writer writer;
+
+    public MafRecordWriter(Writer writer) {
+        this.writer = writer;
+    }
+
+    public void write(Iterator<MafRecord> maf) {
+        int line = 0;
+        while (maf.hasNext()) {
+            MafRecord mafRecord = maf.next();
+            LinkedHashMap<String, String> mafRow = new LinkedHashMap<>();
+            mafRow.put("Hugo_Symbol", mafRecord.hugoSymbol());
+            mafRow.put("Entrez_Gene_Id", mafRecord.entrezGeneId());
+            mafRow.put("Center", mafRecord.center());
+            mafRow.put("NCBI_Build", mafRecord.ncbiBuild());
+            mafRow.put("Chromosome", mafRecord.chromosome());
+            mafRow.put("Start_Position", mafRecord.startPosition().toString());
+            mafRow.put("End_Position", mafRecord.endPosition().toString());
+            mafRow.put("Strand", mafRecord.strand());
+            mafRow.put("Variant_Classification", mafRecord.variantClassification());
+            mafRow.put("Variant_Type", mafRecord.variantType()); 
+            mafRow.put("Reference_Allele", mafRecord.referenceAllele());
+            mafRow.put("Tumor_Seq_Allele1", mafRecord.tumorSeqAllele1());
+            mafRow.put("Tumor_Seq_Allele2", mafRecord.tumorSeqAllele2());
+            mafRow.put("dbSNP_RS", mafRecord.dbSnpRs());
+            mafRow.put("dbSNP_Val_Status", mafRecord.dbSnpValStatus());
+            mafRow.put("Tumor_Sample_Barcode", mafRecord.tumorSampleBarcode());
+            mafRow.put("Matched_Norm_Sample_Barcode", mafRecord.matchedNormSampleBarcode());
+            mafRow.put("Match_Norm_Seq_Allele1", mafRecord.matchNormSeqAllele1());
+            mafRow.put("Match_Norm_Seq_Allele2", mafRecord.matchNormSeqAllele2());
+            mafRow.put("Tumor_Validation_Allele1", mafRecord.tumorValidationAllele1());
+            mafRow.put("Tumor_Validation_Allele2", mafRecord.tumorValidationAllele2());
+            mafRow.put("Match_Norm_Validation_Allele1", mafRecord.matchNormValidationAllele1());
+            mafRow.put("Match_Norm_Validation_Allele2", mafRecord.matchNormValidationAllele2());
+            mafRow.put("Verification_Status", mafRecord.verificationStatus());
+            mafRow.put("Validation_Status", mafRecord.validationStatus());
+            mafRow.put("Mutation_Status", mafRecord.mutationStatus());
+            mafRow.put("Sequencing_Phase", mafRecord.sequencingPhase());
+            mafRow.put("Sequence_Source", mafRecord.sequenceSource());
+            mafRow.put("Validation_Method", mafRecord.validationMethod());
+            mafRow.put("Score", mafRecord.score());
+            mafRow.put("BAM_File", mafRecord.bamFile());
+            mafRow.put("Sequencer", mafRecord.sequencer());
+            mafRow.put("HGVSc_Short", mafRecord.hgvspShort());
+            mafRow.put("t_alt_count", mafRecord.tAltCount().toString());
+            mafRow.put("t_ref_count", mafRecord.tRefCount().toString());
+            mafRow.put("n_alt_count", mafRecord.nAltCount().toString());
+            mafRow.put("n_ref_count", mafRecord.nRefCount().toString());
+            if (line == 0) {
+                writeRow(mafRow.sequencedKeySet());
+            }
+            writeRow(mafRow.sequencedValues());
+            line++;
+        }
+    }
+
+    private void writeRow(Iterable<String> row) {
+        try {
+            writer.write(composeRow(row));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+}

src/main/java/org/cbioportal/file/export/TSVUtil.java

@@ -0,0 +1,13 @@
+package org.cbioportal.file.export;
+
+import java.util.stream.Collectors;
+import java.util.stream.StreamSupport;
+
+public class TSVUtil {
+    public static final String TAB = "\t";
+
+    public static String composeRow(Iterable<String> row) {
+        return StreamSupport.stream(row.spliterator(), false)
+            .map(s -> s.replace(TAB, "\\t")).collect(Collectors.joining(TAB)) + "\n";
+    }
+}

src/main/java/org/cbioportal/file/model/MafRecord.java

@@ -0,0 +1,191 @@
+package org.cbioportal.file.model;
+
+/**
+ * Represents a record in a Mutation Annotation Format (MAF) file.
+ */
+public record MafRecord(
+    /**
+     * A HUGO gene symbol.
+     */
+    String hugoSymbol,
+
+    /**
+     * A Entrez Gene identifier.
+     */
+    String entrezGeneId,
+
+    /**
+     * The sequencing center.
+     */
+    String center,
+
+    /**
+     * The Genome Reference Consortium Build used by a variant calling software. It must be "GRCh37" or "GRCh38" for a human, and "GRCm38" for a mouse.
+     */
+    String ncbiBuild,
+
+    /**
+     * A chromosome number, e.g., "7".
+     */
+    String chromosome,
+
+    /**
+     * Start position of event.
+     */
+    Integer startPosition,
+
+    /**
+     * End position of event.
+     */
+    Integer endPosition,
+
+    /**
+     * We assume that the mutation is reported for the + strand.
+     */
+    String strand,
+
+    /**
+     * Translational effect of variant allele, e.g. Missense_Mutation, Silent, etc.
+     */
+    String variantClassification,
+
+    /**
+     * Variant Type, e.g. SNP, DNP, etc.
+     */
+    String variantType,
+
+    /**
+     * The plus strand reference allele at this position.
+     */
+    String referenceAllele,
+
+    /**
+     * Primary data genotype.
+     */
+    String tumorSeqAllele1,
+
+    /**
+     * Primary data genotype.
+     */
+    String tumorSeqAllele2,
+
+    /**
+     * Latest dbSNP rs ID.
+     */
+    String dbSnpRs,
+
+    /**
+     * dbSNP validation status.
+     */
+    String dbSnpValStatus,
+
+    /**
+     * This is the sample ID. Either a TCGA barcode (patient identifier will be extracted), or for non-TCGA data, a literal SAMPLE_ID as listed in the clinical data file.
+     */
+    String tumorSampleBarcode,
+
+    /**
+     * The sample ID for the matched normal sample.
+     */
+    String matchedNormSampleBarcode,
+
+    /**
+     * Primary data.
+     */
+    String matchNormSeqAllele1,
+
+    /**
+     * Primary data.
+     */
+    String matchNormSeqAllele2,
+
+    /**
+     * Secondary data from orthogonal technology.
+     */
+    String tumorValidationAllele1,
+
+    /**
+     * Secondary data from orthogonal technology.
+     */
+    String tumorValidationAllele2,
+
+    /**
+     * Secondary data from orthogonal technology.
+     */
+    String matchNormValidationAllele1,
+
+    /**
+     * Secondary data from orthogonal technology.
+     */
+    String matchNormValidationAllele2,
+
+    /**
+     * Second pass results from independent attempt using same methods as primary data source. "Verified", "Unknown" or "NA".
+     */
+    String verificationStatus,
+
+    /**
+     * Second pass results from orthogonal technology. "Valid", "Invalid", "Untested", "Inconclusive", "Redacted", "Unknown" or "NA".
+     */
+    String validationStatus,
+
+    /**
+     * "Somatic" or "Germline" are supported by the UI in Mutations tab. "None", "LOH" and "Wildtype" will not be loaded. Other values will be displayed as text.
+     */
+    String mutationStatus,
+
+    /**
+     * Indicates current sequencing phase.
+     */
+    String sequencingPhase,
+
+    /**
+     * Molecular assay type used to produce the analytes used for sequencing.
+     */
+    String sequenceSource,
+
+    /**
+     * The assay platforms used for the validation call.
+     */
+    String validationMethod,
+
+    /**
+     * Not used.
+     */
+    String score,
+
+    /**
+     * Not used.
+     */
+    String bamFile,
+
+    /**
+     * Instrument used to produce primary data.
+     */
+    String sequencer,
+
+    /**
+     * Amino Acid Change, e.g. p.V600E.
+     */
+    String hgvspShort,
+
+    /**
+     * Variant allele count (tumor).
+     */
+    Integer tAltCount,
+
+    /**
+     * Reference allele count (tumor).
+     */
+    Integer tRefCount,
+
+    /**
+     * Variant allele count (normal).
+     */
+    Integer nAltCount,
+
+    /**
+     * Reference allele count (normal).
+     */
+    Integer nRefCount
+) {}

src/test/java/org/cbioportal/file/export/MafRecordWriterTest.java

@@ -0,0 +1,66 @@
+package org.cbioportal.file.export;
+
+import org.cbioportal.file.model.MafRecord;
+import org.junit.Test;
+
+import java.io.StringWriter;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+public class MafRecordWriterTest {
+
+    StringWriter output = new StringWriter();
+    MafRecordWriter writer = new MafRecordWriter(output);
+
+    @Test
+    public void testClinicalAttributeDataWriter() {
+        writer.write(List.of(
+            new MafRecord(
+                "HUGO",
+                "12345", 
+                "center1", 
+                "hg38", 
+                "X", 
+                1000000, 
+                1000100, 
+                "+",
+                "Missense_Mutation",
+                "SNP",
+                "T",
+                "C",
+                "A",
+                "DBSNPRS123",
+                "byFrequency",
+                "SAMPLE_1",
+                "SAMPLE_2",
+                "A",
+                "T",
+                "C",
+                "G",
+                "A",
+                "T",
+                "Verified",
+                "Somatic",
+                "Somatic",
+                "Phase1",
+                "Exome",
+                "Sanger",
+                "1.1",
+                "bam_file",
+                "Illumina hiseq 2000",
+                "SHRT",
+                55,
+                33,
+                100,
+                99
+            )
+        ).iterator());
+
+        assertEquals("""
+            Hugo_Symbol\tEntrez_Gene_Id\tCenter\tNCBI_Build\tChromosome\tStart_Position\tEnd_Position\tStrand\tVariant_Classification\tVariant_Type\tReference_Allele\tTumor_Seq_Allele1\tTumor_Seq_Allele2\tdbSNP_RS\tdbSNP_Val_Status\tTumor_Sample_Barcode\tMatched_Norm_Sample_Barcode\tMatch_Norm_Seq_Allele1\tMatch_Norm_Seq_Allele2\tTumor_Validation_Allele1\tTumor_Validation_Allele2\tMatch_Norm_Validation_Allele1\tMatch_Norm_Validation_Allele2\tVerification_Status\tValidation_Status\tMutation_Status\tSequencing_Phase\tSequence_Source\tValidation_Method\tScore\tBAM_File\tSequencer\tHGVSc_Short\tt_alt_count\tt_ref_count\tn_alt_count\tn_ref_count
+            HUGO\t12345\tcenter1\thg38\tX\t1000000\t1000100\t+\tMissense_Mutation\tSNP\tT\tC\tA\tDBSNPRS123\tbyFrequency\tSAMPLE_1\tSAMPLE_2\tA\tT\tC\tG\tA\tT\tVerified\tSomatic\tSomatic\tPhase1\tExome\tSanger\t1.1\tbam_file\tIllumina hiseq 2000\tSHRT\t55\t33\t100\t99
+            """, output.toString());
+    }
+
+}