adding unit tests for unmapped reads with and without SEQ/QUAL fields.

code format and imports organized according to intellij style

merged htsjdk.samtools.cram.structure with v3

merged htsjdk.samtools.cram.io with v3

merged htsjdk.samtools.cram.lossy with v3

merged htsjdk.samtools.cram.ref with v3

merged htsjdk.samtools.cram.encoding with v3

merged htsjdk.samtools.cram.build with v3

merged htsjdk.samtools.cram.index with v3

added deps and CRC32 files to git; minor fixes in cram/build and slice classes

added  cram/digest package and code format/import to cram package

fixed CramFileWriter test to pass; added swing inspector for CRAM files;

minor updates and moved index and inspector stuff to another project

removed cram.mask package as unused; moved CRC32 streams to io package

javadoc and cleanup in cram.io.Bit*putStream API

cram.io package and CRAM Block class reworked: clean up, re-format, ITF8 and LTF8 tests;

Cram container IO separated from CramIO; CramHeader and versioning re-worked

relaxed assert tests for original vs restored roundtrip of SAM records while writing CRAM.

added support for SAM supplementary 0x800 bit flag

rebased and added SubsMatrix tests

merged htsjdk.samtools.cram.structure with v3

merged htsjdk.samtools.cram.lossy with v3

merged htsjdk.samtools.cram.ref with v3

merged htsjdk.samtools.cram.encoding with v3

merged htsjdk.samtools.cram.build with v3

merged htsjdk.samtools.cram.index with v3

added deps and CRC32 files to git; minor fixes in cram/build and slice classes

fixed CramFileWriter test to pass; added swing inspector for CRAM files;

minor updates and moved index and inspector stuff to another project

removed cram.mask package as unused; moved CRC32 streams to io package

javadoc and cleanup in cram.io.Bit*putStream API

cram.io package and CRAM Block class reworked: clean up, re-format, ITF8 and LTF8 tests;

Cram container IO separated from CramIO; CramHeader and versioning re-worked

added CF 0x8 bit flag to pass CramFileWriterTest

working on indexing test

cram index scan test passes

scan optmizied; working on queryUnmapped: the last bin points to prev container

queryUnmapped test passes now

added static method for indexing CRAM files

fixed javadoc and style

set validation to silent while running index test

code style,  javadocs and minor fixes in CRAMFileIndexTest

adding cram test file for index tests

adding an input stream to continuously read a collection of chunks

CoordSpanInputStream and tests

fixed nof bits returned from int writing methods

index building while writing cram and tests

added ByteArraySeekableStream, used in testing

fix for NPE in CHF due to exernalID used instead of tag id when building codecs

fixed illegal call to iterator.next when delegate is exhausted

fixed NPE in finish() due to missing indexer (required only for random access)

fixed testIteratorFromFileSpan test, it was caught in an eternal loop

added tests for CoordSpanInputStream

technical commit

fix for cramtools issue 20

fix for cramtools issue 25

fixed endiannes in Crc32Hasher used in ContentDigests (BD/SD)

index fixes and tests

spring cleaning 1

cleaned huffint package

cleaned encoding.rans packages

cleaned encoding.read_features package

cleaned encoding.reader package

cleaned encoding.writer package and added DataReader javadocs

cleaned the rest of encoding package

cleaned the rest of encoding package

cleaned cram.io package

cleaned cram.lossy package

cleaned cram.ref package

cleaned cram.structure package

cleaning cram package

minor adjustments to the cram index tests

added lossy tests

added CRAMEdgeCasesTest and minor fixes here and there, mainly inspired by JB cross-tests

fix for N operator: skip ref bases when restore bases in cram

fix for seq id for unmapped placed reads

fix for Gamma failing on zero-len read features

adding cram tests;
fix for triplets and minor adjustments

code style update

minor bug fixes introduced by the last code cleaning

adding test CRAM files generated with htslib and read-compare tests

minor fixes for CRAM index tests

Fix compile errors from rebase. 4 Test still failing.

Setting default validation stringency was affecting downstream tests.

Housekeeping on cram code base.
Updated non java standard variables and packages.

Rename variable.

Removed misc.xml

Revert iml

Revert ipr

Revert other iml

build.xml

@@ -39,11 +39,7 @@
     <property name="javac.debug" value="true"/>
 
     <!-- Get GIT hash, if available, otherwise leave it blank.  -->
-    <exec executable="git" outputproperty="repository.revision" failifexecutionfails="true" errorproperty="">
-        <arg value="log"/>
-        <arg value="-1"/>
-        <arg value="--pretty=format:%H_%at"/>
-    </exec>
+
     <property name="repository.revision" value=""/>
     <property name="htsjdk-version" value="1.132"/>
     <property name="htsjdk-version-file" value="htsjdk.version.properties"/>

src/java/htsjdk/samtools/BinaryTagCodec.java

@@ -267,7 +267,7 @@ private void writeArray(final Object value, final boolean isUnsignedArray) {
      * @param length How many bytes in binaryRep are tag storage.
      */
     public static SAMBinaryTagAndValue readTags(final byte[] binaryRep, final int offset,
-                                         final int length, final ValidationStringency validationStringency) {
+                                                final int length, final ValidationStringency validationStringency) {
         final ByteBuffer byteBuffer = ByteBuffer.wrap(binaryRep, offset, length);
         byteBuffer.order(ByteOrder.LITTLE_ENDIAN);