[DECA-12] Improve I/O bindings.

Resolves #12. * Bump to Hadoop-BAM 7.9.1, net.fnothaft fork. * Add s3a file system bindings.
bigdatagenomics · Sep 14, 2017 · aa6c073 · aa6c073
1 parent 31385e8
commit aa6c073
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Showing 3 changed files with 24 additions and 3 deletions.
diff --git a/deca-cli/pom.xml b/deca-cli/pom.xml
@@ -147,6 +147,10 @@
   </build>
 
   <dependencies>
+    <dependency>
+      <groupId>net.fnothaft</groupId>
+      <artifactId>jsr203-s3a</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
       <artifactId>utils-cli-spark2_2.11</artifactId>

diff --git a/deca-core/pom.xml b/deca-core/pom.xml
@@ -158,7 +158,7 @@
       <artifactId>breeze-natives_${scala.version.prefix}</artifactId>
     </dependency>
     <dependency>
-      <groupId>org.seqdoop</groupId>
+      <groupId>net.fnothaft</groupId>
       <artifactId>hadoop-bam</artifactId>
     </dependency>
     <dependency>

diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,7 @@
     <breeze.version>0.12</breeze.version>
     <!-- Edit the following line to configure the Hadoop (HDFS) version. -->
     <hadoop.version>2.7.3</hadoop.version>
-    <hadoop-bam.version>7.8.0</hadoop-bam.version>
+    <hadoop-bam.version>7.9.1</hadoop-bam.version>
     <utils.version>0.2.11</utils.version>
     <htsjdk.version>2.9.1</htsjdk.version>
     <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
@@ -331,6 +331,11 @@
         <artifactId>utils-metrics-spark2_2.11</artifactId>
         <version>${utils.version}</version>
       </dependency>
+      <dependency>
+        <groupId>net.fnothaft</groupId>
+        <artifactId>jsr203-s3a</artifactId>
+        <version>0.0.1</version>
+      </dependency>
       <dependency>
         <groupId>org.apache.hadoop</groupId>
         <artifactId>hadoop-client</artifactId>
@@ -367,11 +372,23 @@
         <groupId>org.bdgenomics.adam</groupId>
         <artifactId>adam-core-spark2_2.11</artifactId>
         <version>${adam.version}</version>
+        <exclusions>
+          <exclusion>
+            <groupId>org.seqdoop</groupId>
+            <artifactId>hadoop-bam</artifactId>
+          </exclusion>
+        </exclusions>
       </dependency>
       <dependency>
         <groupId>org.bdgenomics.adam</groupId>
         <artifactId>adam-cli-spark2_2.11</artifactId>
         <version>${adam.version}</version>
+        <exclusions>
+          <exclusion>
+            <groupId>org.seqdoop</groupId>
+            <artifactId>hadoop-bam</artifactId>
+          </exclusion>
+        </exclusions>
       </dependency>
       <dependency>
         <groupId>org.scalatest</groupId>
@@ -416,7 +433,7 @@
         <version>${breeze.version}</version>
       </dependency>
       <dependency>
-        <groupId>org.seqdoop</groupId>
+        <groupId>net.fnothaft</groupId>
         <artifactId>hadoop-bam</artifactId>
         <version>${hadoop-bam.version}</version>
         <exclusions>