.gitignore

@@ -10,6 +10,7 @@ src/htsjdk.iml
 *.iml
 *.ipr
 *.iws
+out/
 
 
 

debian/changelog

-htsjdk (2.12.0+dfsg-1) UNRELEASED; urgency=medium
+htsjdk (2.14.3+dfsg-1) UNRELEASED_targeting_experimental; urgency=medium
 
   [ Andreas Tille ]
+  * New upstream version
+    Closes: #894289 (FIXME: check this!)
   * cme fix dpkg-control
-  * Standards-Version: 4.1.1
+  * Standards-Version: 4.1.3
+ 
   [ Olivier Sallou ]
   * d/patches/30-disable-scalatest.patch
     Disable scala testing as scalatest is not available in Debian yet
@@ -10,9 +13,7 @@ htsjdk (2.12.0+dfsg-1) UNRELEASED; urgency=medium
     Disable unit testing due to gradle+testng errors in gradle 3.2
     gradle 3.4 will fix the problem
 
-  WARNING: htsjdk 2.12 breaks API and is not compatible with picard-tools 2.8.1
-
- -- Andreas Tille <tille@debian.org>  Wed, 01 Nov 2017 09:09:56 +0000
+ -- Andreas Tille <tille@debian.org>  Wed, 28 Mar 2018 14:19:04 +0200
 
 htsjdk (2.8.1+dfsg-2) unstable; urgency=medium
 

debian/control

@@ -24,7 +24,7 @@ Build-Depends: default-jdk (>= 2:1.8),
                junit4,
                libjimfs-java,
                scala-library
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htsjdk.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/htsjdk.git
 Homepage: http://samtools.github.io/htsjdk/

debian/htsjdk.pom

@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>com.github.samtools</groupId>
   <artifactId>htsjdk</artifactId>
-  <version>2.5.0</version>
+  <version>2.14.3</version>
   <name>HTSJDK</name>
   <description>A Java API for high-throughput sequencing data (HTS) formats</description>
   <url>http://samtools.github.io/htsjdk/</url>
@@ -27,18 +27,36 @@
     <url>git@github.com:samtools/htsjdk.git</url>
   </scm>
   <dependencies>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-jexl</artifactId>
+      <version>2.1.1</version>
+      <scope>compile</scope>
+    </dependency>
     <dependency>
       <groupId>commons-logging</groupId>
       <artifactId>commons-logging</artifactId>
       <version>1.1.1</version>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>org.xerial.snappy</groupId>
+      <artifactId>snappy-java</artifactId>
+      <version>1.1.4</version>
+      <scope>compile</scope>
+    </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-compress</artifactId>
       <version>1.4.1</version>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>org.tukaani</groupId>
+      <artifactId>xz</artifactId>
+      <version>1.5</version>
+      <scope>compile</scope>
+    </dependency>
     <dependency>
       <groupId>gov.nih.nlm.ncbi</groupId>
       <artifactId>ngs-java</artifactId>
@@ -46,10 +64,16 @@
       <scope>compile</scope>
     </dependency>
     <dependency>
-      <groupId>org.tukaani</groupId>
-      <artifactId>xz</artifactId>
-      <version>1.5</version>
-      <scope>compile</scope>
+      <groupId>org.scala-lang</groupId>
+      <artifactId>scala-library</artifactId>
+      <version>2.12.1</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.scalatest</groupId>
+      <artifactId>scalatest_2.12</artifactId>
+      <version>3.0.1</version>
+      <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.testng</groupId>
@@ -58,16 +82,16 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-jexl</artifactId>
-      <version>2.1.1</version>
-      <scope>compile</scope>
+      <groupId>com.google.jimfs</groupId>
+      <artifactId>jimfs</artifactId>
+      <version>1.1</version>
+      <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>org.xerial.snappy</groupId>
-      <artifactId>snappy-java</artifactId>
-      <version>1.0.3-rc3</version>
-      <scope>compile</scope>
+      <groupId>org.pegdown</groupId>
+      <artifactId>pegdown</artifactId>
+      <version>1.4.2</version>
+      <scope>test</scope>
     </dependency>
   </dependencies>
 </project>

debian/htsjdk.pom.asc

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-=jlsl
+iQIcBAABAgAGBQJafMM1AAoJEHqkTkuxf2donbAP/1ntOikZk6SBuYr58gnLUkKW
+Ll7ptC6YdsqkshTo8DS/Ize5s5IKuyILMD7D/mz+yECt/wdWuySzfwmKYj3nnMhy
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+5EFQD1P9nj/mf1LbA0BSQVfuYeYvTSIz+vw+AUx6ums2HIFUZyTQBLhgdG7Qyvgk
+Z+BH1id17u9euVB7Gnhp
+=sAvZ
 -----END PGP SIGNATURE-----

debian/patches/30-disable-scalatest.patch

@@ -6,7 +6,7 @@ Forwarded: not-needed
 Last-Updated: 2017-10-18
 --- a/build.gradle
 +++ b/build.gradle
-@@ -6,7 +6,7 @@
+@@ -6,7 +6,7 @@ buildscript {
  
  plugins {
      id 'java'
@@ -15,7 +15,7 @@ Last-Updated: 2017-10-18
      id 'maven'
      id 'signing'
  }
-@@ -23,11 +23,11 @@
+@@ -23,11 +23,11 @@ dependencies {
      compile "org.tukaani:xz:1.5"
      compile "gov.nih.nlm.ncbi:ngs-java:1.2.4"
  
@@ -32,7 +32,7 @@ Last-Updated: 2017-10-18
   }
  
  sourceCompatibility = 1.8
-@@ -90,22 +90,20 @@
+@@ -90,22 +90,20 @@ test {
          jvmArgs += '-Dsamjdk.sra_libraries_download=true'
      }
  

src/main/java/htsjdk/samtools/BAMFileWriter.java

@@ -29,7 +29,6 @@ import htsjdk.samtools.util.IOUtil;
 import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.samtools.util.zip.DeflaterFactory;
 
-import java.io.DataOutputStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
@@ -37,7 +36,6 @@ import java.io.StringWriter;
 import java.io.Writer;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 
 /**
  * Concrete implementation of SAMFileWriter for writing gzipped BAM files.
@@ -51,37 +49,37 @@ class BAMFileWriter extends SAMFileWriterImpl {
 
     protected BAMFileWriter(final File path) {
         blockCompressedOutputStream = new BlockCompressedOutputStream(path);
-        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
         outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
     }
 
     protected BAMFileWriter(final File path, final int compressionLevel) {
         blockCompressedOutputStream = new BlockCompressedOutputStream(path, compressionLevel);
-        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
         outputBinaryCodec.setOutputFileName(path.getAbsolutePath());
     }
 
     protected BAMFileWriter(final OutputStream os, final File file) {
         blockCompressedOutputStream = new BlockCompressedOutputStream(os, file);
-        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
         outputBinaryCodec.setOutputFileName(getPathString(file));
     }
 
     protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel) {
         blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel);
-        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
         outputBinaryCodec.setOutputFileName(getPathString(file));
     }
 
     protected BAMFileWriter(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
         blockCompressedOutputStream = new BlockCompressedOutputStream(os, file, compressionLevel, deflaterFactory);
-        outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
         outputBinaryCodec.setOutputFileName(getPathString(file));
     }
 
     protected BAMFileWriter(final OutputStream os, final String absoluteFilename, final int compressionLevel, final DeflaterFactory deflaterFactory) {
       blockCompressedOutputStream = new BlockCompressedOutputStream(os, null, compressionLevel, deflaterFactory);
-      outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+      outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
       outputBinaryCodec.setOutputFileName(absoluteFilename);
     }
 
@@ -204,7 +202,7 @@ class BAMFileWriter extends SAMFileWriterImpl {
 
     protected static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {
         final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);
-        final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream));
+        final BinaryCodec outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);
         writeHeader(outputBinaryCodec, samFileHeader);
         try {
             blockCompressedOutputStream.flush();

src/main/java/htsjdk/samtools/Defaults.java

@@ -110,7 +110,7 @@ public class Defaults {
         }
         REFERENCE_FASTA = getFileProperty("reference_fasta", null);
         USE_CRAM_REF_DOWNLOAD = getBooleanProperty("use_cram_ref_download", false);
-        EBI_REFERENCE_SERVICE_URL_MASK = "http://www.ebi.ac.uk/ena/cram/md5/%s";
+        EBI_REFERENCE_SERVICE_URL_MASK = "https://www.ebi.ac.uk/ena/cram/md5/%s";
         CUSTOM_READER_FACTORY = getStringProperty("custom_reader", "");
         SAM_FLAG_FIELD_FORMAT = SamFlagField.valueOf(getStringProperty("sam_flag_field_format", SamFlagField.DECIMAL.name()));
         SRA_LIBRARIES_DOWNLOAD = getBooleanProperty("sra_libraries_download", false);

src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java

@@ -53,7 +53,7 @@ public class DownsamplingIteratorFactory {
             "strategy to finish. Works in a single pass, and will provide accuracy close to (but often not as good as) HighAccuracy while requiring " +
             "memory proportional to the set of reads emitted from the ConstantMemory strategy to the HighAccuracy strategy. Works well when downsampling " +
             "large inputs to small proportions (e.g. downsampling hundreds of millions of reads and retaining only 2%. Should be accurate 99.9% of the time " +
-            "when the input contains >= 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead.";
+            "when the input contains more than 50,000 templates (read names). For smaller inputs, HighAccuracy is recommended instead.";
 
     /** Describes the available downsampling strategies. */
     public enum Strategy {

src/main/java/htsjdk/samtools/NotPrimarySkippingIterator.java

@@ -24,39 +24,17 @@
 package htsjdk.samtools;
 
 import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.samtools.util.PeekIterator;
 
 /**
  * Wrapper around SAMRecord iterator that skips over non-primary elements.
  * This iterator conflates a filtering iterator and a peekable iterator.  It would be cleaner to
  * handle those concerns separately.
+ * @deprecated use {@link SecondaryAlignmentSkippingIterator} instead.
  */
-public class NotPrimarySkippingIterator {
-    private final PeekIterator<SAMRecord> it;
+@Deprecated
+public class NotPrimarySkippingIterator extends SecondaryAlignmentSkippingIterator {
 
-    public NotPrimarySkippingIterator(final CloseableIterator<SAMRecord> underlyingIt) {
-        it = new PeekIterator<SAMRecord>(underlyingIt);
-        skipAnyNotprimary();
-    }
-
-    public boolean hasCurrent() {
-        return it.hasNext();
-    }
-
-    public SAMRecord getCurrent() {
-        assert(hasCurrent());
-        return it.peek();
-    }
-
-    public boolean advance() {
-        it.next();
-        skipAnyNotprimary();
-        return hasCurrent();
-    }
-
-    private void skipAnyNotprimary() {
-        while (it.hasNext() && it.peek().getNotPrimaryAlignmentFlag()) {
-            it.next();
-        }
+    public NotPrimarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt) {
+        super(underlyingIt);
     }
 }

src/main/java/htsjdk/samtools/SAMFileHeader.java

@@ -148,9 +148,11 @@ public class SAMFileHeader extends AbstractSAMHeaderRecord
 
     /**
      * Look up sequence record by name.
+     * @return sequence record if it's found by name,
+     * or null if sequence dictionary is empty or if the sequence is not found in the dictionary.
      */
     public SAMSequenceRecord getSequence(final String name) {
-        return mSequenceDictionary.getSequence(name);
+        return mSequenceDictionary == null ? null : mSequenceDictionary.getSequence(name);
     }
 
     /**

src/main/java/htsjdk/samtools/SAMFileWriterFactory.java

@@ -32,7 +32,6 @@ import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.samtools.util.zip.DeflaterFactory;
 
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.file.Files;
@@ -300,7 +299,7 @@ public class SAMFileWriterFactory implements Cloneable {
             if (this.useAsyncIo) return new AsyncSAMFileWriter(ret, this.asyncOutputBufferSize);
             else return ret;
         } catch (final IOException ioe) {
-            throw new RuntimeIOException("Error opening file: " + outputPath.toUri());
+            throw new RuntimeIOException("Error opening file: " + outputPath.toUri(), ioe);
         }
     }
 
@@ -352,7 +351,7 @@ public class SAMFileWriterFactory implements Cloneable {
                                         samFlagFieldOutput);
             return initWriter(header, presorted, ret);
         } catch (final IOException ioe) {
-            throw new RuntimeIOException("Error opening file: " + outputPath.toUri());
+            throw new RuntimeIOException("Error opening file: " + outputPath.toUri(), ioe);
         }
     }
 
@@ -588,7 +587,7 @@ public class SAMFileWriterFactory implements Cloneable {
                     indexOS = Files.newOutputStream(indexPath);
                 }
                 catch (final IOException ioe) {
-                    throw new RuntimeIOException("Error creating index file for: " + indexPath.toUri());
+                    throw new RuntimeIOException("Error creating index file for: " + indexPath.toUri(), ioe);
                 }
             }
         }
@@ -597,7 +596,7 @@ public class SAMFileWriterFactory implements Cloneable {
             cramOS = IOUtil.maybeBufferOutputStream(Files.newOutputStream(outputFile), bufferSize);
         }
         catch (final IOException ioe) {
-            throw new RuntimeIOException("Error creating CRAM file: " + outputFile.toUri());
+            throw new RuntimeIOException("Error creating CRAM file: " + outputFile.toUri(), ioe);
         }
 
         final Path md5Path = IOUtil.addExtension(outputFile, ".md5");

src/main/java/htsjdk/samtools/SAMFlag.java

@@ -39,6 +39,9 @@ public enum SAMFlag {
     MATE_REVERSE_STRAND(            0x20,   "SEQ of the next segment in the template being reverse complemented"),
     FIRST_OF_PAIR(                  0x40,   "The first segment in the template"),
     SECOND_OF_PAIR(                 0x80,   "The last segment in the template"),
+    SECONDARY_ALIGNMENT(            0x100,  "Secondary alignment"),
+    /** @deprecated use {@link #SECONDARY_ALIGNMENT} instead. */
+    @Deprecated
     NOT_PRIMARY_ALIGNMENT(          0x100,  "Secondary alignment"),
     READ_FAILS_VENDOR_QUALITY_CHECK(0x200,  "Not passing quality controls"),
     DUPLICATE_READ(                 0x400,  "PCR or optical duplicate"), 

src/main/java/htsjdk/samtools/SAMRecord.java

@@ -967,9 +967,18 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
 
     /**
      * the alignment is not primary (a read having split hits may have multiple primary alignment records).
+     * @deprecated use {@link #isSecondaryAlignment()} instead.
      */
+    @Deprecated
     public boolean getNotPrimaryAlignmentFlag() {
-        return (mFlags & SAMFlag.NOT_PRIMARY_ALIGNMENT.flag) != 0;
+        return isSecondaryAlignment();
+    }
+
+    /**
+     * the alignment is secondary (a read having slipt hits have multiple alignment records).
+     */
+    public boolean isSecondaryAlignment() {
+        return (mFlags & SAMFlag.SECONDARY_ALIGNMENT.flag) != 0;
     }
 
     /**
@@ -1063,9 +1072,18 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
 
     /**
      * the alignment is not primary (a read having split hits may have multiple primary alignment records).
+     * @deprecated use {@link #setSecondaryAlignment(boolean)} instead.
      */
+    @Deprecated
     public void setNotPrimaryAlignmentFlag(final boolean flag) {
-        setFlag(flag, SAMFlag.NOT_PRIMARY_ALIGNMENT.flag);
+        setSecondaryAlignment(flag);
+    }
+
+    /**
+     * the alignment is secondary (a read having slipt hits have multiple alignment records).
+     */
+    public void setSecondaryAlignment(final boolean flag) {
+        setFlag(flag, SAMFlag.SECONDARY_ALIGNMENT.flag);
     }
 
     /**
@@ -1094,7 +1112,7 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
      * equivalent to {@code (getNotPrimaryAlignmentFlag() || getSupplementaryAlignmentFlag())}.
      */
     public boolean isSecondaryOrSupplementary() {
-        return getNotPrimaryAlignmentFlag() || getSupplementaryAlignmentFlag();
+        return isSecondaryAlignment() || getSupplementaryAlignmentFlag();
     }
 
     private void setFlag(final boolean flag, final int bit) {
@@ -1954,9 +1972,9 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
             if (firstOnly) return ret;
         }
         if (getReadUnmappedFlag()) {
-            if (getNotPrimaryAlignmentFlag()) {
+            if (isSecondaryAlignment()) {
                 if (ret == null) ret = new ArrayList<>();
-                ret.add(new SAMValidationError(SAMValidationError.Type.INVALID_FLAG_NOT_PRIM_ALIGNMENT, "Not primary alignment flag should not be set for unmapped read.", getReadName()));
+                ret.add(new SAMValidationError(SAMValidationError.Type.INVALID_FLAG_NOT_PRIM_ALIGNMENT, "Secondary alignment flag should not be set for unmapped read.", getReadName()));
                 if (firstOnly) return ret;
             }
             if (getSupplementaryAlignmentFlag()) {
@@ -2030,7 +2048,7 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
             if (firstOnly) return ret;
         }
         // TODO(mccowan): Is this asking "is this the primary alignment"?
-        if (this.getReadLength() == 0 && !this.getNotPrimaryAlignmentFlag()) {
+        if (this.getReadLength() == 0 && !this.isSecondaryAlignment()) {
             final Object fz = getAttribute(SAMTagUtil.getSingleton().FZ);
             if (fz == null) {
                 final String cq = (String)getAttribute(SAMTagUtil.getSingleton().CQ);
@@ -2083,7 +2101,7 @@ public class SAMRecord implements Cloneable, Locatable, Serializable {
             if (firstOnly) return ret;
         }
 
-        if (getCigar().getReadLength() != 0 && getCigar().getReadLength() != getReadLength()) {
+        if (getReadLength() != 0 && getCigar().getReadLength() != 0 && getCigar().getReadLength() != getReadLength()) {
             if (ret == null) ret = new ArrayList<>();
             ret.add(new SAMValidationError(SAMValidationError.Type.MISMATCH_CIGAR_SEQ_LENGTH,
                     "CIGAR covers " + getCigar().getReadLength() + " bases but the sequence is " + getReadLength() + " read bases ",

src/main/java/htsjdk/samtools/SAMRecordQueryNameComparator.java

@@ -51,8 +51,8 @@ public class SAMRecordQueryNameComparator implements SAMRecordComparator, Serial
         if (samRecord1.getReadNegativeStrandFlag() != samRecord2.getReadNegativeStrandFlag()) {
             return (samRecord1.getReadNegativeStrandFlag()? 1: -1);
         }
-        if (samRecord1.getNotPrimaryAlignmentFlag() != samRecord2.getNotPrimaryAlignmentFlag()) {
-            return samRecord2.getNotPrimaryAlignmentFlag()? -1: 1;
+        if (samRecord1.isSecondaryAlignment() != samRecord2.isSecondaryAlignment()) {
+            return samRecord2.isSecondaryAlignment()? -1: 1;
         }
         if (samRecord1.getSupplementaryAlignmentFlag() != samRecord2.getSupplementaryAlignmentFlag()) {
             return samRecord2.getSupplementaryAlignmentFlag() ? -1 : 1;

src/main/java/htsjdk/samtools/SAMRecordSetBuilder.java

@@ -25,9 +25,9 @@ package htsjdk.samtools;
 
 import htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy;
 import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.samtools.util.CoordMath;
 import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.samtools.util.SequenceUtil;
+import htsjdk.samtools.util.TestUtil;
 
 import java.io.File;
 import java.io.IOException;
@@ -58,7 +58,7 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
     private static final byte[] BASES = {'A', 'C', 'G', 'T'};
     private static final String READ_GROUP_ID = "1";
     private static final String SAMPLE = "FREE_SAMPLE";
-    private final Random random = new Random();
+    private final Random random = new Random(TestUtil.RANDOM_SEED);
 
     private SAMFileHeader header;
     private final Collection<SAMRecord> records;
@@ -287,7 +287,7 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
                              final boolean recordUnmapped, final String cigar, final String qualityString,
                              final int defaultQuality, final boolean isSecondary) throws SAMException {
         final htsjdk.samtools.SAMRecord rec = createReadNoFlag(name, contig, start, negativeStrand, recordUnmapped, cigar, qualityString, defaultQuality);
-        if (isSecondary) rec.setNotPrimaryAlignmentFlag(true);
+        if (isSecondary) rec.setSecondaryAlignment(true);
         this.records.add(rec);
         return rec;
     }
@@ -300,7 +300,7 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
                              final boolean recordUnmapped, final String cigar, final String qualityString,
                              final int defaultQuality, final boolean isSecondary, final boolean isSupplementary) throws SAMException {
         final htsjdk.samtools.SAMRecord rec = createReadNoFlag(name, contig, start, negativeStrand, recordUnmapped, cigar, qualityString, defaultQuality);
-        if (isSecondary) rec.setNotPrimaryAlignmentFlag(true);
+        if (isSecondary) rec.setSecondaryAlignment(true);
         if (isSupplementary) rec.setSupplementaryAlignmentFlag(true);
         this.records.add(rec);
         return rec;
@@ -434,11 +434,11 @@ public class SAMRecordSetBuilder implements Iterable<SAMRecord> {
         end2.setReadPairedFlag(true);
         end2.setSecondOfPairFlag(true);
 
-        if (record1NonPrimary) end1.setNotPrimaryAlignmentFlag(true);
-        if (record2NonPrimary) end2.setNotPrimaryAlignmentFlag(true);
+        if (record1NonPrimary) end1.setSecondaryAlignment(true);
+        if (record2NonPrimary) end2.setSecondaryAlignment(true);
 
-        if (record1NonPrimary) end1.setNotPrimaryAlignmentFlag(true);
-        if (record2NonPrimary) end2.setNotPrimaryAlignmentFlag(true);
+        if (record1NonPrimary) end1.setSecondaryAlignment(true);
+        if (record2NonPrimary) end2.setSecondaryAlignment(true);
 
         // set mate info
         SamPairUtil.setMateInfo(end1, end2, true);

src/main/java/htsjdk/samtools/SAMRecordUtil.java

-/*
- * The MIT License
- *
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-package htsjdk.samtools;
-
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
-
-/**
- *
- * @author alecw@broadinstitute.org
- *
- * @deprecated 10/27/2016 Use {@link SAMRecord} constants and functions
- */
-@Deprecated
-public class SAMRecordUtil {
-    /**
-     * @deprecated 6/5/2017 Use {@link SAMRecord#TAGS_TO_REVERSE_COMPLEMENT}
-     */
-    @Deprecated
-    public static List<String> TAGS_TO_REVERSE_COMPLEMENT = Arrays.asList(SAMTag.E2.name(), SAMTag.SQ.name());
-
-    /**
-     * @deprecated 6/5/2017 Use {@link SAMRecord#TAGS_TO_REVERSE}
-     */
-    @Deprecated
-    public static List<String> TAGS_TO_REVERSE            = Arrays.asList(SAMTag.OQ.name(), SAMTag.U2.name());
-
-    /**
-     * Reverse-complement bases and reverse quality scores along with known optional attributes that
-     * need the same treatment. Changes made in-place, instead of making a copy of the bases, qualities,
-     * or attributes. If a copy is needed use {@link #reverseComplement(SAMRecord, boolean)}.
-     * See {@link #TAGS_TO_REVERSE_COMPLEMENT} {@link #TAGS_TO_REVERSE}
-     * for the default set of tags that are handled.
-     *
-     * @deprecated  6/5/2017 Use {@link SAMRecord#reverseComplement} but note that the default behavior there is different
-     * It will default to making a copy, not reverse-complementing in-place!
-     */
-    @Deprecated
-    public static void reverseComplement(final SAMRecord rec) {
-        rec.reverseComplement(TAGS_TO_REVERSE_COMPLEMENT, TAGS_TO_REVERSE, true);
-    }
-
-    /**
-     * Reverse-complement bases and reverse quality scores along with known optional attributes that
-     * need the same treatment. Optionally makes a copy of the bases, qualities or attributes instead
-     * of altering them in-place. See {@link #TAGS_TO_REVERSE_COMPLEMENT} {@link #TAGS_TO_REVERSE}
-     * for the default set of tags that are handled.
-     *
-     * @param rec Record to reverse complement.
-     * @param inplace Setting this to false will clone all attributes, bases and qualities before changing the values.
-     *
-     * @deprecated  6/5/2017 Use {@link SAMRecord#reverseComplement}
-     */
-    @Deprecated
-    public static void reverseComplement(final SAMRecord rec, boolean inplace) {
-        rec.reverseComplement(TAGS_TO_REVERSE_COMPLEMENT, TAGS_TO_REVERSE, inplace);
-    }
-
-    /**
-     * Reverse complement bases and reverse quality scores. In addition reverse complement any
-     * non-null attributes specified by tagsToRevcomp and reverse and non-null attributes
-     * specified by tagsToReverse.
-     *
-     * @deprecated  6/5/2017 Use {@link SAMRecord#reverseComplement}
-     */
-    @Deprecated
-    public static void reverseComplement(final SAMRecord rec, final Collection<String> tagsToRevcomp, final Collection<String> tagsToReverse, boolean inplace) {
-        rec.reverseComplement(tagsToRevcomp, tagsToReverse, inplace);
-    }
-}

src/main/java/htsjdk/samtools/SAMUtils.java

@@ -580,7 +580,7 @@ public final class SAMUtils {
         rec.setCigarString(SAMRecord.NO_ALIGNMENT_CIGAR);
         rec.setMappingQuality(SAMRecord.NO_MAPPING_QUALITY);
         rec.setInferredInsertSize(0);
-        rec.setNotPrimaryAlignmentFlag(false);
+        rec.setSecondaryAlignment(false);
         rec.setSupplementaryAlignmentFlag(false);
         rec.setProperPairFlag(false);
         rec.setReadUnmappedFlag(true);