Remove deprecated SAMRecord.format() and now-dead helpers.

SAMRecord.format() was deprecated in favor of getSAMString() because it didn't
guarantee a valid SAM text representation. Now that getSAMString() is the
canonical formatter (and is used by toString()), drop format() and the private
helpers that supported it: addField, formatTagValue, safeEquals.

Also remove the SRALazyRecord.format() override, which existed only because
format() bypassed lazy attribute loading; getSAMString() goes through
SRALazyRecord.getBinaryAttributes() which already handles lazy loading. And
delete a couple of stale commented-out debug prints that referenced format().

BREAKING CHANGE: SAMRecord.format() has been removed. Callers should use
SAMRecord.getSAMString() instead.

Author: tfenne

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

@@ -1840,82 +1840,6 @@ public int getAttributesBinarySize() {
         return -1;
     }
 
-    /**
-     *
-     * @return String representation of this.
-     * @deprecated This method is not guaranteed to return a valid SAM text representation of the SAMRecord.
-     * To get standard SAM text representation, {@link SAMRecord#getSAMString}.
-     */
-    @Deprecated
-    public String format() {
-        final StringBuilder buffer = new StringBuilder();
-        addField(buffer, getReadName(), null, null);
-        addField(buffer, getFlags(), null, null);
-        addField(buffer, getReferenceName(), null, "*");
-        addField(buffer, getAlignmentStart(), 0, "*");
-        addField(buffer, getMappingQuality(), 0, "0");
-        addField(buffer, getCigarString(), null, "*");
-        addField(buffer, getMateReferenceName(), null, "*");
-        addField(buffer, getMateAlignmentStart(), 0, "*");
-        addField(buffer, getInferredInsertSize(), 0, "*");
-        addField(buffer, getReadString(), null, "*");
-        addField(buffer, getBaseQualityString(), null, "*");
-        if (mAttributes != null) {
-            SAMBinaryTagAndValue entry = getBinaryAttributes();
-            while (entry != null) {
-                addField(buffer, formatTagValue(entry.tag, entry.value));
-                entry = entry.getNext();
-            }
-        }
-        return buffer.toString();
-    }
-
-    private void addField(final StringBuilder buffer, final Object value, final Object defaultValue, final String defaultString) {
-        if (safeEquals(value, defaultValue)) {
-            addField(buffer, defaultString);
-        } else if (value == null) {
-            addField(buffer, "");
-        } else {
-            addField(buffer, value.toString());
-        }
-    }
-
-    private void addField(final StringBuilder buffer, final String field) {
-        if (buffer.length() > 0) {
-            buffer.append('\t');
-        }
-        buffer.append(field);
-    }
-
-    private static String formatTagValue(final short tag, final Object value) {
-        final String tagString = SAMTag.makeStringTag(tag);
-        if (value == null || value instanceof String) {
-            return tagString + ":Z:" + value;
-        } else if (value instanceof Integer || value instanceof Long ||
-                value instanceof Short || value instanceof Byte) {
-            return tagString + ":i:" + value;
-        } else if (value instanceof Character) {
-            return tagString + ":A:" + value;
-        } else if (value instanceof Float) {
-            return tagString + ":f:" + value;
-        } else if (value instanceof byte[]) {
-            return tagString + ":H:" + StringUtil.bytesToHexString((byte[]) value);
-        } else {
-            throw new RuntimeException("Unexpected value type for tag " + tagString +
-                    ": " + value + " of class " + value.getClass().getName());
-        }
-    }
-
-    private boolean safeEquals(final Object o1, final Object o2) {
-        if (o1 == o2) {
-            return true;
-        } else if (o1 == null || o2 == null) {
-            return false;
-        } else {
-            return o1.equals(o2);
-        }
-    }
-
     /**
      * Force all lazily-initialized data members to be initialized.  If a subclass overrides this method,
      * typically it should also call  super method.

src/main/java/htsjdk/samtools/sra/SRALazyRecord.java

@@ -725,14 +725,6 @@ public Object clone() throws CloneNotSupportedException {
         return newObject;
     }
 
-    @Override
-    public String format() {
-        if (!initializedAttributes.contains(LazyAttribute.RG)) {
-            getAttribute("RG");
-        }
-        return super.format();
-    }
-
     @Override
     public List<SAMValidationError> isValid(final boolean firstOnly) {
         loadFields();

src/test/java/htsjdk/samtools/BAMFileIndexTest.java

@@ -418,9 +418,6 @@ private int runQueryTest(final File bamFile, final String sequence, final int st
                 record2 = iter2.next();
                 count2++;
             }
-            // System.out.println("Iteration:");
-            // System.out.println(" Record1 = " + ((record1 == null) ? "null" : record1.format()));
-            // System.out.println(" Record2 = " + ((record2 == null) ? "null" : record2.format()));
             if (record1 == null && record2 == null) {
                 break;
             }

src/test/java/htsjdk/samtools/BAMRemoteFileTest.java

@@ -169,7 +169,6 @@ private void runLocalRemoteTest(final URL bamURL, final File bamFile, final Stri
         assertTrue(records1.size() > 0);
         assertEquals(records1.size(), records2.size());
         for (int i = 0; i < records1.size(); i++) {
-            //System.out.println(records1.get(i).format());
             assertEquals(records1.get(i).getSAMString(), records2.get(i).getSAMString());
         }
     }