Change SAMTextHeaderCodec to no longer accumulate the entire text of … (

#1361)

* Change SAMTextHeaderCodec to no longer accumulate the entire text of the header into memory.

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

@@ -187,16 +187,12 @@ protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAM
     }
 
     /**
-     * Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the
-     * samFileHeader and the String, use the version of this method which takes both.
+     * Writes a header to a BAM file.
      */
     protected static void writeHeader(final BinaryCodec outputBinaryCodec, final SAMFileHeader samFileHeader) {
-        // Do not use SAMFileHeader.getTextHeader() as it is not updated when changes to the underlying object are made
-        final String headerString;
         final Writer stringWriter = new StringWriter();
         new SAMTextHeaderCodec().encode(stringWriter, samFileHeader, true);
-        headerString = stringWriter.toString();
-
+        final String headerString = stringWriter.toString();
         writeHeader(outputBinaryCodec, samFileHeader, headerString);
     }
 

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

@@ -101,7 +101,6 @@ public enum GroupOrder {
     private final Map<String, SAMProgramRecord> mProgramRecordMap = new HashMap<>();
     private SAMSequenceDictionary mSequenceDictionary = new SAMSequenceDictionary();
     final private List<String> mComments = new ArrayList<>();
-    private String textHeader;
     private final List<SAMValidationError> mValidationErrors = new ArrayList<>();
 
     public SAMFileHeader() {
@@ -322,24 +321,11 @@ public void setAttribute(final String key, final String value) {
         super.setAttribute(key, tempVal);
     }
 
-    /**
-     * If this SAMHeader was read from a file, this property contains the header
-     * as it appeared in the file, otherwise it is null.  Note that this is not a toString()
-     * operation.  Changes to the SAMFileHeader object after reading from the file are not reflected in this value.
-     *
-     * In addition this value is only set if one of the following is true:
-     *   - The size of the header is < 1,048,576 characters (1MB ascii, 2MB unicode)
-     *   - There are either validation or parsing errors associated with the header
-     *
-     * Invalid header lines may appear in value but are not stored in the SAMFileHeader object.
-     */
-    public String getTextHeader() {
-        return textHeader;
-    }
+    /** @deprecated since May 1st 2019 - text version of header is no longer stored. */
+    @Deprecated public String getTextHeader() {  return null; }
 
-    public void setTextHeader(final String textHeader) {
-        this.textHeader = textHeader;
-    }
+    /** @deprecated since May 1st 2019 - text version of header is no longer stored. */
+    @Deprecated public void setTextHeader(final String textHeader) { }
 
     public List<String> getComments() {
         return Collections.unmodifiableList(mComments);

src/main/java/htsjdk/samtools/SAMTextHeaderCodec.java

@@ -24,6 +24,7 @@
 package htsjdk.samtools;
 
 import htsjdk.samtools.SAMFileHeader.SortOrder;
+import htsjdk.samtools.SAMValidationError.Type;
 import htsjdk.samtools.util.DateParser;
 import htsjdk.samtools.util.LineReader;
 import htsjdk.samtools.util.RuntimeIOException;
@@ -55,8 +56,6 @@ public class SAMTextHeaderCodec {
     private String mSource;
     private List<SAMSequenceRecord> sequences;
     private List<SAMReadGroupRecord> readGroups;
-    // Accumulate header while reading it from input.
-    private final StringBuilder textHeader = new StringBuilder();
 
     // For error reporting when parsing
     private ValidationStringency validationStringency = ValidationStringency.SILENT;
@@ -124,23 +123,14 @@ public SAMFileHeader decode(final LineReader reader, final String source) {
         mFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences));
         mFileHeader.setReadGroups(readGroups);
 
-        // Only store the header text if there was a parsing error or the it's less than 1MB on disk / 2MB in mem
-        if (!mFileHeader.getValidationErrors().isEmpty() || textHeader.length() < (1024 * 1024)) {
-            mFileHeader.setTextHeader(textHeader.toString());
-        }
-
         SAMUtils.processValidationErrors(mFileHeader.getValidationErrors(), -1, validationStringency);
         return mFileHeader;
     }
 
     private String advanceLine() {
         final int nextChar = mReader.peek();
-        if (nextChar != '@') {
-            return null;
-        }
-        mCurrentLine = mReader.readLine();
-        textHeader.append(mCurrentLine).append('\n');
-        return mCurrentLine;
+        this.mCurrentLine = (nextChar == '@') ? mReader.readLine() : null;
+        return this.mCurrentLine;
     }
 
     /**
@@ -547,4 +537,4 @@ public void setValidationStringency(final ValidationStringency validationStringe
         }
         this.validationStringency = validationStringency;
     }
-}
+}