Clean some deprecated classes/methods usages in htsjdk

src/main/java/htsjdk/samtools/SamPairUtil.java

@@ -182,6 +182,15 @@ public static int computeInsertSize(final SAMRecord firstEnd, final SAMRecord se
     }
 
     /**
+     * Write the mate info for two SAMRecords.  This will always clear/remove any mate cigar tag that is present.
+     * @param rec1 the first SAM record
+     * @param rec2 the second SAM record
+     */
+    public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2) {
+        setMateInfo(rec1, rec2, false);
+    }
+
+    /**
      * Write the mate info for two SAMRecords
      * @param rec1 the first SAM record. Must have a non-null SAMFileHeader.
      * @param rec2 the second SAM record. Must have a non-null SAMFileHeader.
@@ -270,6 +279,7 @@ else if (rec1.getReadUnmappedFlag() && rec2.getReadUnmappedFlag()) {
      * @param rec2 the second SAM record
      * @param header the SAM file header
      * @param setMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
+     * @deprecated use {@link #setMateInfo(SAMRecord, SAMRecord, boolean)} instead
      */
     @Deprecated
     public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header, final boolean setMateCigar) {
@@ -281,9 +291,11 @@ public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final
      * @param rec1 the first SAM record
      * @param rec2 the second SAM record
      * @param header the SAM file header
+     * @deprecated use {@link #setMateInfo(SAMRecord, SAMRecord)} instead
      */
+    @Deprecated
     public static void setMateInfo(final SAMRecord rec1, final SAMRecord rec2, final SAMFileHeader header) {
-        setMateInfo(rec1, rec2, false);
+        setMateInfo(rec1, rec2);
     }
 
     /**
@@ -322,26 +334,43 @@ public static void setMateInformationOnSupplementalAlignment( final SAMRecord su
 
     /**
      * This method will clear any mate cigar already present.
+     * @deprecated use {@link #setProperPairAndMateInfo(SAMRecord, SAMRecord, List)} instead
      */
+    @Deprecated
     public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
                                                 final SAMFileHeader header,
-                                                final List<PairOrientation> exepectedOrientations) {
-        setProperPairAndMateInfo(rec1, rec2, header, exepectedOrientations, false);
+                                                final List<PairOrientation> expectedOrientations) {
+        setProperPairAndMateInfo(rec1, rec2, expectedOrientations);
     }
 
     /**
-     * @param rec1
-     * @param rec2
-     * @param header
-     * @param exepectedOrientations
      * @param addMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
+     * @deprecated use {@link #setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)}
      */
+    @Deprecated
     public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
                                                 final SAMFileHeader header,
-                                                final List<PairOrientation> exepectedOrientations,
+                                                final List<PairOrientation> expectedOrientations,
+                                                final boolean addMateCigar) {
+        setProperPairAndMateInfo(rec1, rec2, expectedOrientations, addMateCigar);
+    }
+
+    /**
+     * This method will clear any mate cigar already present.
+     */
+    public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
+                                                final List<PairOrientation> expectedOrientations) {
+        setProperPairAndMateInfo(rec1, rec2, expectedOrientations, false);
+    }
+
+    /**
+     * @param addMateCigar true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
+     */
+    public static void setProperPairAndMateInfo(final SAMRecord rec1, final SAMRecord rec2,
+                                                final List<PairOrientation> expectedOrientations,
                                                 final boolean addMateCigar) {
-        setMateInfo(rec1, rec2, header, addMateCigar);
-        setProperPairFlags(rec1, rec2, exepectedOrientations);
+        setMateInfo(rec1, rec2, addMateCigar);
+        setProperPairFlags(rec1, rec2, expectedOrientations);
     }
 
     public static void setProperPairFlags(final SAMRecord rec1, final SAMRecord rec2, final List<PairOrientation> expectedOrientations) {

src/main/java/htsjdk/samtools/util/CollectionUtil.java

@@ -104,16 +104,22 @@ private void initializeKeyIfUninitialized(final K k) {
     /**
      * Partitions a collection into groups based on a characteristics of that group.  Partitions are embodied in a map, whose keys are the
      * value of that characteristic, and the values are the partition of elements whose characteristic evaluate to that key.
+     *
+     * @deprecated use java8 .stream().collect(Collectors.groupingBy(()-> function)) instead
      */
-    @Deprecated //use java8 .stream().collect(Collectors.groupingBy(()-> function)) instead
+    @Deprecated
     public static <K, V> Map<K, Collection<V>> partition(final Collection<V> collection, final Partitioner<V, K> p) {
         final MultiMap<K, V> partitionToValues = new MultiMap<>();
         for (final V entry : collection) {
             partitionToValues.append(p.getPartition(entry), entry);
         }
         return partitionToValues;
     }
-    @Deprecated //not needed, use Collectors.groupingBy instead
+
+    /**
+     * @deprecated use Collectors.groupingBy instead
+     */
+    @Deprecated
     public static abstract class Partitioner<V, K> {
         public abstract K getPartition(final V v);
     }

src/main/java/htsjdk/samtools/util/IOUtil.java

@@ -71,7 +71,7 @@
  */
 public class IOUtil {
     /**
-     * @deprecated Use Defaults.NON_ZERO_BUFFER_SIZE instead.
+     * @deprecated Use {@link Defaults#NON_ZERO_BUFFER_SIZE} instead.
      */
     @Deprecated
     public static final int STANDARD_BUFFER_SIZE = Defaults.NON_ZERO_BUFFER_SIZE;

src/main/java/htsjdk/samtools/util/IntervalList.java

@@ -102,9 +102,14 @@ public void addall(final Collection<Interval> intervals) {
         }
     }
 
-    /** Sorts the internal collection of intervals by coordinate. */
-    @Deprecated // Use sorted() instead of sort(). The sort() function modifies the object in-place and
-    // is therefore difficult to work with. sorted() returns a new IntervalList that is sorted
+    /**
+     * Sorts the internal collection of intervals by coordinate.
+     *
+     * Note: this function modifies the object in-place and is therefore difficult to work with.
+     *
+     * @deprecated use {@link #sorted()} instead.
+     */
+    @Deprecated
     public void sort() {
         Collections.sort(this.intervals, new IntervalCoordinateComparator(this.header));
         this.header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
@@ -154,19 +159,27 @@ public IntervalList uniqued(final boolean concatenateNames) {
         return value;
     }
 
-    /** Sorts and uniques the list of intervals held within this interval list. */
-    @Deprecated//use uniqued() instead. This function modifies the object in-place and
-    // is therefore difficult to work with.
+    /**
+     * Sorts and uniques the list of intervals held within this interval list.
+     *
+     * Note: this function modifies the object in-place and is therefore difficult to work with.
+     *
+     * @deprecated use {@link #uniqued()} instead.
+     */
+    @Deprecated
     public void unique() {
         unique(true);
     }
 
     /**
      * Sorts and uniques the list of intervals held within this interval list.
+     *
+     * Note: this function modifies the object in-place and is therefore difficult to work with.
+     *
      * @param concatenateNames If false, interval names are not concatenated when merging intervals to save space.
+     * @deprecated use {@link #uniqued(boolean)} instead.
      */
-    @Deprecated//use uniqued() instead. This function modifies the object in-place and
-    // is therefore difficult to work with
+    @Deprecated
     public void unique(final boolean concatenateNames) {
         sort();
         final List<Interval> tmp = getUniqueIntervals(concatenateNames);
@@ -186,10 +199,12 @@ public void unique(final boolean concatenateNames) {
      *
      * Note: has the side-effect of sorting the stored intervals in coordinate order if not already sorted.
      *
+     * Note: this function modifies the object in-place and is therefore difficult to work with.
+     *
      * @return the set of unique intervals condensed from the contained intervals
+     * @deprecated use {@link #uniqued()#getIntervals()} instead.
      */
-    @Deprecated//use uniqued().getIntervals() instead. This function modifies the object in-place and
-    // is therefore difficult to work with
+    @Deprecated
     public List<Interval> getUniqueIntervals() {
         return getUniqueIntervals(true);
     }
@@ -249,14 +264,14 @@ else if (current.intersects(next) || current.abuts(next)) {
     }
 
     /**
-     * Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
-     * @param concatenateNames If false, the merged interval has the name of the earlier interval.  This keeps name shorter.
-     */
-    @Deprecated //use uniqued(concatenateNames).getIntervals() or the static version instead to avoid changing the underlying object.
-    /**
-     * Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
-     * @param concatenateNames If false, the merged interval has the name of the earlier interval.  This keeps name shorter.
+     * Merges list of intervals and reduces them like {@link #getUniqueIntervals()}.
+     *
+     * Note: this function modifies the object in-place and is therefore difficult to work with.
+     *
+     * @param concatenateNames If false, the merged interval has the name of the earlier interval. This keeps name shorter.
+     * @deprecated use {@link #uniqued(boolean)#getIntervals()} or {@link #getUniqueIntervals(IntervalList, boolean)} instead.
      */
+    @Deprecated
     public List<Interval> getUniqueIntervals(final boolean concatenateNames) {
         if (getHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
             sort();

src/main/java/htsjdk/tribble/Feature.java

@@ -36,6 +36,8 @@
      * @deprecated use getContig() instead
      */
     @Deprecated
-    public String getChr();
+    default public String getChr() {
+        return getContig();
+    }
 
 }

src/main/java/htsjdk/tribble/SimpleFeature.java

@@ -39,11 +39,6 @@ public SimpleFeature(final String contig, final int start, final int end) {
         this.end = end;
     }
 
-    @Deprecated
-    public String getChr() {
-        return contig;
-    }
-
     public String getContig() {
         return contig;
     }

src/main/java/htsjdk/tribble/bed/SimpleBEDFeature.java

@@ -51,14 +51,6 @@ public SimpleBEDFeature(int start, int end, String chr) {
         this.chr = chr;
     }
 
-
-    @Deprecated
-    @Override
-    public String getChr() {
-        return getContig();
-    }
-
-
     @Override
     public String getContig() {
         return chr;

src/main/java/htsjdk/tribble/example/CountRecords.java

@@ -193,12 +193,8 @@ public static FeatureCodec getFeatureCodec(File featureFile) {
         //    return new VCFCodec();
         if (featureFile.getName().endsWith(".bed") || featureFile.getName().endsWith(".BED") )
             return new BEDCodec();
-        //if (featureFile.getName().endsWith(".snp") || featureFile.getName().endsWith(".rod") )
-        //    return new OldDbSNPCodec();
         if (featureFile.getName().endsWith(".geli.calls") || featureFile.getName().endsWith(".geli") )
             return new GeliTextCodec();
-        //if (featureFile.getName().endsWith(".txt") || featureFile.getName().endsWith(".TXT") )
-        //    return new SoapSNPCodec();
         throw new IllegalArgumentException("Unable to determine correct file type based on the file name, for file -> " + featureFile);
     }
 }

src/main/java/htsjdk/tribble/example/ExampleBinaryCodec.java

@@ -118,7 +118,7 @@ public boolean canDecode(final String path) {
         Iterator<FEATURE_TYPE> it = reader.iterator();
         while ( it.hasNext() ) {
             final Feature f = it.next();
-            dos.writeUTF(f.getChr());
+            dos.writeUTF(f.getContig());
             dos.writeInt(f.getStart());
             dos.writeInt(f.getEnd());
         }

src/main/java/htsjdk/tribble/gelitext/GeliTextFeature.java

@@ -83,12 +83,6 @@ public GeliTextFeature(String contig,
         this.likelihoods = likelihoods;
     }
 
-    /** Return the features reference sequence name, e.g chromosome or contig */
-    @Deprecated
-    public String getChr() {
-        return getContig();
-    }
-
     @Override
     public String getContig() {
         return this.contig;

src/main/java/htsjdk/tribble/index/IndexFactory.java

@@ -345,8 +345,8 @@ private static Index createIndex(final File inputFile, final FeatureIterator ite
 
             checkSorted(inputFile, lastFeature, currentFeature);
             //should only visit chromosomes once
-            final String curChr = currentFeature.getChr();
-            final String lastChr = lastFeature != null ? lastFeature.getChr() : null;
+            final String curChr = currentFeature.getContig();
+            final String lastChr = lastFeature != null ? lastFeature.getContig() : null;
             if(!curChr.equals(lastChr)){
                 if(visitedChromos.containsKey(curChr)){
                     String msg = "Input file must have contiguous chromosomes.";
@@ -369,15 +369,15 @@ private static Index createIndex(final File inputFile, final FeatureIterator ite
     }
 
     private static String featToString(final Feature feature){
-        return feature.getChr() + ":" + feature.getStart() + "-" + feature.getEnd();
+        return feature.getContig() + ":" + feature.getStart() + "-" + feature.getEnd();
     }
 
     private static void checkSorted(final File inputFile, final Feature lastFeature, final Feature currentFeature){
         // if the last currentFeature is after the current currentFeature, exception out
-        if (lastFeature != null && currentFeature.getStart() < lastFeature.getStart() && lastFeature.getChr().equals(currentFeature.getChr()))
+        if (lastFeature != null && currentFeature.getStart() < lastFeature.getStart() && lastFeature.getContig().equals(currentFeature.getContig()))
             throw new TribbleException.MalformedFeatureFile("Input file is not sorted by start position. \n" +
-                    "We saw a record with a start of " + currentFeature.getChr() + ":" + currentFeature.getStart() +
-                    " after a record with a start of " + lastFeature.getChr() + ":" + lastFeature.getStart(), inputFile.getAbsolutePath());
+                    "We saw a record with a start of " + currentFeature.getContig() + ":" + currentFeature.getStart() +
+                    " after a record with a start of " + lastFeature.getContig() + ":" + lastFeature.getStart(), inputFile.getAbsolutePath());
     }
 
 

src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java

@@ -64,13 +64,13 @@ public IntervalIndexCreator(final File inputFile) {
 
     public void addFeature(final Feature feature, final long filePosition) {
         // if we don't have a chrIndex yet, or if the last one was for the previous contig, create a new one
-        if (chrList.isEmpty() || !chrList.getLast().getName().equals(feature.getChr())) {
+        if (chrList.isEmpty() || !chrList.getLast().getName().equals(feature.getContig())) {
             // if we're creating a new chrIndex (not the first), make sure to dump the intervals to the old chrIndex
             if (!chrList.isEmpty())
                 addIntervalsToLastChr(filePosition);
 
             // create a new chr index for the current contig
-            chrList.add(new ChrIndex(feature.getChr()));
+            chrList.add(new ChrIndex(feature.getContig()));
             intervals.clear();
         }
 

src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java

@@ -66,14 +66,14 @@ public LinearIndexCreator(final File inputFile) {
      */
     public void addFeature(final Feature feature, final long filePosition) {
         // fi we don't have a chrIndex yet, or if the last one was for the previous contig, create a new one
-        if (chrList.isEmpty() || !chrList.getLast().getName().equals(feature.getChr())) {
+        if (chrList.isEmpty() || !chrList.getLast().getName().equals(feature.getContig())) {
             // if we're creating a new chrIndex (not the first), make sure to dump the blocks to the old chrIndex
             if (!chrList.isEmpty())
                 for (int x = 0; x < blocks.size(); x++) {
                     blocks.get(x).setEndPosition((x + 1 == blocks.size()) ? filePosition : blocks.get(x + 1).getStartPosition());
                     chrList.getLast().addBlock(blocks.get(x));
                 }
-            chrList.add(new LinearIndex.ChrIndex(feature.getChr(),binWidth));
+            chrList.add(new LinearIndex.ChrIndex(feature.getContig(),binWidth));
             blocks.clear();
 
             // Add the first block

src/main/java/htsjdk/tribble/index/tabix/TabixIndexCreator.java

@@ -73,7 +73,7 @@ public TabixIndexCreator(final TabixFormat formatSpec) {
 
     @Override
     public void addFeature(final Feature feature, final long filePosition) {
-        final String sequenceName = feature.getChr();
+        final String sequenceName = feature.getContig();
         final int referenceIndex;
         if (sequenceName.equals(currentSequenceName)) {
             referenceIndex = sequenceNames.size() - 1;

src/main/java/htsjdk/variant/variantcontext/VariantContext.java

@@ -342,7 +342,7 @@
      * @param other the VariantContext to copy
      */
     protected VariantContext(VariantContext other) {
-        this(other.getSource(), other.getID(), other.getChr(), other.getStart(), other.getEnd(),
+        this(other.getSource(), other.getID(), other.getContig(), other.getStart(), other.getEnd(),
                 other.getAlleles(), other.getGenotypes(), other.getLog10PError(),
                 other.getFiltersMaybeNull(),
                 other.getAttributes(),
@@ -1653,10 +1653,6 @@ private final Genotype fullyDecodeGenotypes(final Genotype g, final VCFHeader he
     // tribble integration routines -- not for public consumption
     //
     // ---------------------------------------------------------------------------------------------------------
-    @Deprecated
-    public String getChr() {
-        return getContig();
-    }
 
     @Override
     public String getContig() {

src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java

@@ -84,7 +84,7 @@ public int compare(final VariantContext firstVariantContext, final VariantContex
 		// present. This error checking should already have been done in the constructor but it's left
 		// in as defence anyway.
 		final int contigCompare =
-				this.contigIndexLookup.get(firstVariantContext.getChr()) - this.contigIndexLookup.get(secondVariantContext.getChr());
+				this.contigIndexLookup.get(firstVariantContext.getContig()) - this.contigIndexLookup.get(secondVariantContext.getContig());
 		return contigCompare != 0
 				? contigCompare
 				: firstVariantContext.getStart() - secondVariantContext.getStart();

src/main/java/htsjdk/variant/variantcontext/VariantJEXLContext.java

@@ -59,7 +59,7 @@
 
     static {
         attributes.put("vc", (VariantContext vc) -> vc);
-        attributes.put("CHROM", VariantContext::getChr);
+        attributes.put("CHROM", VariantContext::getContig);
         attributes.put("POS", VariantContext::getStart);
         attributes.put("TYPE", (VariantContext vc) -> vc.getType().toString());
         attributes.put("QUAL", (VariantContext vc) -> -10 * vc.getLog10PError());