Proposal to evolve to HTSJDK version 3 (DO NOT MERGE)

htsjdk3-dev/htsjdk-core/README.md

@@ -0,0 +1,7 @@
+# HTSJDK-CORE
+
+Contains common code and interface/api definitions.
+
+Includes SAM/BAM, VCF and tribble support.
+
+Should not include significant dependencies.

htsjdk3-dev/htsjdk-core/src/main/java/htsjdk/samtools/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * Contains SAM support.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+package htsjdk.samtools;

htsjdk3-dev/htsjdk-core/src/main/java/htsjdk/tribble/Feature.java

@@ -0,0 +1,35 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2017 Daniel Gomez-Sanchez
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+package htsjdk.tribble;
+
+
+import htsjdk.util.Locatable;
+
+/**
+ * Marker interface for Locatables with Tribble support. A Feature represents a record in a tribble-supported file format.
+ * As {@link Locatable}, represents a locus on a reference sequence and is expected to return 1-based closed-ended intervals.
+ */
+public interface Feature extends Locatable {
+
+}

htsjdk3-dev/htsjdk-core/src/main/java/htsjdk/tribble/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * Support for indexed and query-able genomic file formats.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+package htsjdk.tribble;

htsjdk3-dev/htsjdk-core/src/main/java/htsjdk/util/Locatable.java

@@ -0,0 +1,48 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2017 Daniel Gomez-Sanchez
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package htsjdk.util;
+
+/**
+ * Any class that has a single logical mapping onto the genome should implement Locatable
+ * positions should be reported as 1-based and closed at both ends.
+ */
+public interface Locatable {
+
+    /**
+     * Gets the contig name for the contig this is mapped to.  May return null if there is no unique mapping.
+     * @return name of the contig this is mapped to, potentially null
+     */
+    String getContig();
+
+    /**
+     * @return 1-based start position, undefined if getContig() == null
+     */
+    int getStart();
+
+    /**
+     * @return 1-based closed-ended position, undefined if getContig() == null
+     */
+    int getEnd();
+}

htsjdk3-dev/htsjdk-core/src/main/java/htsjdk/util/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * Common utilies.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+package htsjdk.util;

htsjdk3-dev/htsjdk-core/src/main/java/htsjdk/variant/package-info.java

@@ -0,0 +1,6 @@
+/**
+ *
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+package htsjdk.variant;

htsjdk3-dev/htsjdk-cram/README.md

@@ -0,0 +1,3 @@
+# HTSJDK-CRAM
+
+Includes support for CRAM format.

htsjdk3-dev/htsjdk-cram/src/main/java/htsjdk/samtools/cram/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * Support for CRAM format.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+package htsjdk.samtools.cram;

htsjdk3-dev/htsjdk-jexl/README.md

@@ -0,0 +1,3 @@
+# HTSJDK-JEXL
+
+Includes support for JEXL expressions in VariantContext.

htsjdk3-dev/htsjdk-sra/README.md

@@ -0,0 +1,3 @@
+# HTSJDK-SRA
+
+Includes support for SRA format.

htsjdk3-dev/htsjdk-sra/src/main/java/htsjdk/samtools/sra/package-info.java

@@ -0,0 +1,6 @@
+/**
+ * SRA support.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+package htsjdk.samtools.sra;

src/main/java/htsjdk/Htsjdk3.java

@@ -0,0 +1,31 @@
+package htsjdk;
+
+import java.lang.annotation.Documented;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Marker interface to indicate the status of the class in the HTSJDK3 development.
+ *
+ * @author Daniel Gomez-Sanchez (magicDGS)
+ */
+@Retention(RetentionPolicy.CLASS)
+@Target({
+        ElementType.ANNOTATION_TYPE,
+        ElementType.CONSTRUCTOR,
+        ElementType.FIELD,
+        ElementType.METHOD,
+        ElementType.TYPE
+})
+@Documented
+public @interface Htsjdk3 {
+
+    /** Indicates the name of the new package if changed; if not changed, returns the empty String. */
+    public String newPackage();
+
+    /** Returns {@code true} if the port is backwards compatible; {@code false} otherwise. */
+    public boolean backwardsCompatible();
+
+}

src/main/java/htsjdk/samtools/util/Locatable.java

@@ -1,10 +1,13 @@
 package htsjdk.samtools.util;
 
+import htsjdk.Htsjdk3;
+
 /**
  * Any class that has a single logical mapping onto the genome should implement Locatable
  * positions should be reported as 1-based and closed at both ends
  *
  */
+@Htsjdk3(newPackage = "", backwardsCompatible = true)
 public interface Locatable {
 
     /**

src/main/java/htsjdk/tribble/Feature.java

@@ -24,12 +24,14 @@
 package htsjdk.tribble;
 
 
+import htsjdk.Htsjdk3;
 import htsjdk.samtools.util.Locatable;
 
 /**
  * Marker interface for Locatables with Tribble support. A Feature represents a record in a tribble-supported file format.
  * As {@link Locatable}, represents a locus on a reference sequence and is expected to return 1-based closed-ended intervals.
  */
+@Htsjdk3(newPackage = "", backwardsCompatible = false)
 public interface Feature extends Locatable {
 
     /**