add VFF

settings.gradle

@@ -1,3 +1,3 @@
 rootProject.name = 'bioio'
 
-include 'core', 'bed', 'gff', 'fasta', 'pedigree', 'pdb', 'chain', 'vcf', 'genbank', 'turtle', 'bgee', 'text'
+include 'core', 'bed', 'gff', 'fasta', 'pedigree', 'chain', 'vcf', 'vff', 'genbank', 'turtle', 'bgee', 'text'

vff/build.gradle

@@ -0,0 +1,3 @@
+dependencies {
+    api project(':core')
+}

vff/src/main/java/org/pharmgkb/parsers/vff/VffParser.java

@@ -0,0 +1,68 @@
+package org.pharmgkb.parsers.vff;
+
+import org.pharmgkb.parsers.LineParser;
+import org.pharmgkb.parsers.vff.model.VffEntry;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnegative;
+import javax.annotation.Nonnull;
+import javax.annotation.concurrent.ThreadSafe;
+import java.lang.invoke.MethodHandles;
+import java.util.concurrent.atomic.AtomicLong;
+
+@ThreadSafe
+public class VffParser implements VffParserI {
+
+	private static final long sf_logEvery = 10000;
+	private static final Pattern sf_slash = Pattern.compile("/");
+	private static final Pattern sf_tab = Pattern.compile("\t");
+
+	private static final Logger sf_logger = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
+	private final AtomicLong m_lineNumber = new AtomicLong(0L);
+
+	@Nonnull
+	@Override
+	public VffEntry apply(@Nonnull String line) throws BadDataFormatException {
+
+		if (m_lineNumber.incrementAndGet() % sf_logEvery == 0) {
+			sf_logger.debug("Reading line #{}", m_lineNumber);
+		}
+
+		String[] parts = sf_tab.split(line);
+        String[] alleles = sf_slash.split(parts[3]);
+		try {
+			return new VffEntry(
+                new StandardChromosomeName(parts[0]),
+                Integer.parseInt(parts[1]) - 1,
+                Integer.parseInt(parts[2]) - 1,
+                alleles[0],
+                alleles[1],
+                Strand.fromSymbol(parts[4])
+            )
+
+		} catch (IllegalArgumentException | ArrayIndexOutOfBoundsException e) {
+			throw new BadDataFormatException("Bad data format on line #" + m_lineNumber.get()
+					                                 + "; line is [[[" + line + "]]]", e);
+		} catch (RuntimeException e) {
+			// this is a little weird, but it's helpful
+			// not that we're not throwing a BadDataFormatException because we don't expect AIOOB, e.g.
+			e.addSuppressed(new RuntimeException("Unexpectedly failed to parse line " + m_lineNumber));
+			throw e;
+		}
+	}
+
+	@Nonnegative
+	@Override
+	public long nLinesProcessed() {
+		return m_lineNumber.get();
+	}
+
+    @Override
+    public String toString() {
+        return new StringJoiner(", ", VffParser.class.getSimpleName() + "[", "]")
+            .add("lineNumber=" + m_lineNumber)
+            .toString();
+    }
+}

vff/src/main/java/org/pharmgkb/parsers/vff/VffParserI.java

@@ -0,0 +1,8 @@
+package org.pharmgkb.parsers.vff;
+
+import org.pharmgkb.parsers.LineParser;
+import org.pharmgkb.parsers.vff.model.VffEntry;
+
+public interface VffParserI extends LineParser<VffEntry> {
+
+}

vff/src/main/java/org/pharmgkb/parsers/vff/VffWriter.java

@@ -0,0 +1,44 @@
+package org.pharmgkb.parsers.vff;
+
+import org.pharmgkb.parsers.LineWriter;
+import org.pharmgkb.parsers.vff.model.VffEntry;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.annotation.Nonnegative;
+import javax.annotation.Nonnull;
+import javax.annotation.concurrent.ThreadSafe;
+import java.lang.invoke.MethodHandles;
+import java.util.concurrent.atomic.AtomicLong;
+
+@ThreadSafe
+public class VffWriter implements LineWriter<VffEntry>, VffWriterI {
+
+	private static final long sf_logEvery = 10000;
+	private static final Logger sf_logger = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
+	private final AtomicLong m_lineNumber = new AtomicLong(0L);
+
+	@Nonnull
+	@Override
+	public String apply(@Nonnull VffEntry entry) {
+        return entry.chromosome().original() + "\t"
+            + (entry.start() + 1) + "\t"
+            + (entry.end() + 1) + "\t"
+            + entry.refAllele() + "/" + entry.variantAllele() + "\t"
+            + entry.strand().symbol;
+	}
+
+	@Nonnegative
+	@Override
+	public long nLinesProcessed() {
+		return m_lineNumber.get();
+	}
+
+	@Override
+	public String toString() {
+		return "VffWriter{" +
+				"lineNumber=" + m_lineNumber.get() +
+				'}';
+	}
+}

vff/src/main/java/org/pharmgkb/parsers/vff/VffWriterI.java

@@ -0,0 +1,5 @@
+package org.pharmgkb.parsers.vff;
+
+public interface VffWriterI {
+
+}

vff/src/main/java/org/pharmgkb/parsers/vff/model/VffEntry.java

@@ -0,0 +1,36 @@
+package org.pharmgkb.parsers.vff.model;
+
+import org.pharmgkb.parsers.core.model.NucleotideCode;
+
+import javax.annotation.Nonnegative;
+import javax.annotation.Nonnull;
+
+public record VffEntry(
+    @Nonnull ChromosomeName chromosome,
+    @Nonnegative int start,
+    @Nonnegative int end,
+    @Nonnull String refAllele,
+    @Nonnull String variantAllele,
+    @Nonnull Strand strand
+) {
+
+    @Nonnull
+    public List<NucleotideCode> refBases() {
+        return refAllele.chars().mapToObj(c -> String.valueOf(c)).map(NucleotideCode::valueOf).toList();
+    }
+
+    @Nonnull
+    public List<NucleotideCode> variantBases() {
+        return variantAllele.chars().mapToObj(c -> String.valueOf(c)).map(NucleotideCode::valueOf).toList();
+    }
+
+    @Nonnull
+    public List<NucleotideCode> insertedBases() {
+        return start == end + 1 ? variantBases() : List.empty();
+    }
+
+    @Nonnull
+    public List<NucleotideCode> deleted() {
+        return start == end - 2 ? refBases() : List.empty();
+    }
+}