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htsjdk.samtools.cram.digest.ContentDigests Maven / Gradle / Ivy
package htsjdk.samtools.cram.digest;
import htsjdk.samtools.SAMBinaryTagAndValue;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMTag;
import htsjdk.samtools.cram.structure.CRAMCompressionRecord;
import htsjdk.samtools.util.Log;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.util.Arrays;
import java.util.EnumSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
public final class ContentDigests {
public static final EnumSet ALL = EnumSet
.allOf(KNOWN_DIGESTS.class);
public static final EnumSet CRC32 = EnumSet.of(
KNOWN_DIGESTS.BD, KNOWN_DIGESTS.SD);
private static final Log log = Log.getInstance(ContentDigests.class);
private List digesters = new LinkedList();
public static ContentDigests create(final EnumSet requestedDigests) {
final List digesters = new LinkedList();
for (final KNOWN_DIGESTS digest : requestedDigests)
digesters.add(digest.createDigester());
return new ContentDigests(digesters);
}
public static ContentDigests create(final SAMBinaryTagAndValue binaryTags) {
final List digesters = new LinkedList();
SAMBinaryTagAndValue binaryTag = binaryTags;
while (binaryTag != null) {
final String tagID = SAMTag.makeStringTag(
binaryTag.tag);
final KNOWN_DIGESTS hash;
try {
hash = KNOWN_DIGESTS.valueOf(tagID);
digesters.add(hash.createDigester());
} catch (final IllegalArgumentException e) {
// The tag is not one of the known content digest tags.
}
binaryTag = binaryTag.getNext();
}
return new ContentDigests(digesters);
}
private ContentDigests(final List hashers) {
this.digesters = hashers;
}
void add(final SAMRecord record) {
for (final Digester digester : digesters)
digester.add(record);
}
public void add(final CRAMCompressionRecord record) {
for (final Digester digester : digesters)
digester.addCramRecord(record);
}
public SAMBinaryTagAndValue getAsTags() {
SAMBinaryTagAndValue tag = null;
for (final Digester digester : digesters) {
if (tag == null)
tag = digester.toTag();
else
tag = tag.insert(digester.toTag());
}
return tag;
}
public boolean test(final SAMBinaryTagAndValue tags) {
for (final Digester digester : digesters) {
final SAMBinaryTagAndValue foundTag = tags.find(digester.tagCode);
if (foundTag == null)
continue;
if (!(foundTag.value instanceof byte[]))
throw new RuntimeException("Expecting a byte array but got: "
+ foundTag.value.getClass().getName());
final byte[] expected = (byte[]) foundTag.value;
final byte[] actual = digester.digest.asByteArray();
if (!Arrays.equals(expected, actual)) {
final String expectedString = toHexString(expected);
final String actualString = toHexString(actual);
log.error(String
.format("Content hash mismatch for tag %s, actual: %s; expected: %s",
digester.tagID, actualString, expectedString));
return false;
} else
log.debug("Content digest ok: " + digester.tagID);
}
return true;
}
private static String toHex(final byte[] bytes) {
final StringBuilder sb = new StringBuilder();
for (final byte t : bytes) {
sb.append(String.format(Locale.US, "%02x", (0xFF & t)).toUpperCase()).append(
' ');
}
return sb.toString();
}
private static String toHexString(final byte[] bytes) {
return toHex(bytes).replace(" ", "");
}
private static class Digester {
final AbstractSerialDigest digest;
final SERIES series;
final String tagID;
final short tagCode;
Digester(final AbstractSerialDigest digest, final SERIES series, final String tagID) {
this.digest = digest;
this.series = series;
this.tagID = tagID;
this.tagCode = SAMTag.makeBinaryTag(tagID);
}
void add(final SAMRecord record) {
digest.add(series.getBytes(record));
}
void addCramRecord(final CRAMCompressionRecord record) {
digest.add(series.getBytes(record));
}
SAMBinaryTagAndValue toTag() {
return new SAMBinaryTagAndValue(tagCode, digest.asByteArray());
}
}
public enum KNOWN_DIGESTS {
BD {
@Override
Digester createDigester() {
return new Digester(new Crc32Hasher(new IntegerSumCombine()),
SERIES.BASES, name());
}
},
SD {
@Override
Digester createDigester() {
return new Digester(new Crc32Hasher(new IntegerSumCombine()),
SERIES.SCORES, name());
}
},
B5 {
@Override
Digester createDigester() {
try {
return new Digester(new MessageDigestHasher(
MessageDigest.getInstance("SHA-512"),
new ByteSumCombine(), null), SERIES.BASES, name());
} catch (final NoSuchAlgorithmException e) {
throw new RuntimeException(e);
}
}
},
S5 {
@Override
Digester createDigester() {
try {
return new Digester(new MessageDigestHasher(
MessageDigest.getInstance("SHA-512"),
new ByteSumCombine(), null), SERIES.SCORES, name());
} catch (final NoSuchAlgorithmException e) {
throw new RuntimeException(e);
}
}
},
B1 {
@Override
Digester createDigester() {
try {
return new Digester(new MessageDigestHasher(
MessageDigest.getInstance("SHA-1"),
new ByteSumCombine(), null), SERIES.BASES, name());
} catch (final NoSuchAlgorithmException e) {
throw new RuntimeException(e);
}
}
},
S1 {
@Override
Digester createDigester() {
try {
return new Digester(new MessageDigestHasher(
MessageDigest.getInstance("SHA-1"),
new ByteSumCombine(), null), SERIES.SCORES, name());
} catch (final NoSuchAlgorithmException e) {
throw new RuntimeException(e);
}
}
};
abstract Digester createDigester();
}
}
