Commit 7520c502 authored by Afif Elghraoui's avatar Afif Elghraoui
Browse files

New upstream version 2.1.3+dfsg

parent 6f4bf90d

README.md

+3 −3
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@@ -8,12 +8,12 @@ You must have a recent [JDK](http://www.oracle.com/technetwork/java/javase/down 


    git clone https://github.com/marbl/MHAP.git

    cd MHAP

    maven install

    mvn install

    

For a quick user-quide, run:

Maven executables vary by system, it could also be maven/mvn/mv32, depending on your installation. For a quick user-quide, run:



    cd target

    java -jar mhap-2.1.1.jar

    java -jar mhap-2.1.3.jar



## Docs

For the full documentation information please see http://mhap.readthedocs.io/en/latest/

docs/source/installation.rst

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@@ -28,19 +28,25 @@ The pre-compiled version is recommended to users who want to run MHAP, without d 


.. code-block:: bash



    $ wget https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.tar.gz

    $ wget https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.jar.gz



And if ``wget`` not available, you can use ``curl`` instead:



.. code-block:: bash



    $ curl -L https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.tar.gz > mhap-2.1.1.tar.gz

    $ curl -L https://github.com/marbl/MHAP/releases/download/v2.1.1/mhap-2.1.1.jar.gz



Then run



.. code-block:: bash



   $ tar xvzf mhap-2.1.1.tar.gz

   $ gunzip mhap-2.1.1.jar.gz

   

Now to run mhap



.. code-block:: bash



   $ java -jar mhap-2.1.1.jar



Source

-----------------

pom.xml

+5 −2
Original line number Diff line number Diff line
@@ -3,7 +3,7 @@ 
	<modelVersion>4.0.0</modelVersion>

	<groupId>mhap</groupId>

	<artifactId>mhap</artifactId>

	<version>2.1.1</version>

	<version>2.1.3</version>

	<name>MinHash Alignment Process</name>

	<build>

		<resources>
@@ -134,4 +134,7 @@ 
	</dependencies>

	<url>https://github.com/marbl/MHAP</url>

	<description>MinHash alignment process (MHAP pronounced MAP): locality sensitive hashing to detect overlaps and utilities.</description>

	<properties>

		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

	</properties>

</project>

src/main/java/edu/umd/marbl/mhap/impl/AbstractMatchSearch.java

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@@ -64,7 +64,7 @@ public abstract class AbstractMatchSearch 
		this.sequencesSearched = new AtomicLong();

	}



	protected void addData(final SequenceSketchStreamer data)

	protected void addData(final SequenceSketchStreamer data, boolean doReverseCompliment)

	{

		// figure out number of cores

		ExecutorService execSvc = Executors.newFixedThreadPool(this.numThreads);
@@ -80,7 +80,7 @@ public abstract class AbstractMatchSearch 
					try

					{

						ReadBuffer buf = new ReadBuffer();

						SequenceSketch seqHashes = data.dequeue(false, buf);

						SequenceSketch seqHashes = data.dequeue(!doReverseCompliment, buf);

						while (seqHashes != null)

						{

							addSequence(seqHashes);

src/main/java/edu/umd/marbl/mhap/impl/FastaData.java

+5 −3
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@@ -126,6 +126,7 @@ public class FastaData implements Cloneable 
	{

		StringBuilder fastaSeq = new StringBuilder();

		String header = null;

		long index = -1 - this.offset;

		

		synchronized (this.fileReader)

		{
@@ -175,13 +176,14 @@ public class FastaData implements Cloneable 
				else

					break;

			}



			if (fastaSeq.length()>0)

				index = this.numberProcessed.incrementAndGet();			

		}			

		

		String fastaSeqSring = fastaSeq.toString();

		if (!fastaSeqSring.isEmpty())

		{

			long index = this.numberProcessed.incrementAndGet();

			

			//generate sequence id

			SequenceId id;

			if (SequenceId.STORE_FULL_ID)