Add HtsgetBAMFileReader

.travis.yml

@@ -1,6 +1,8 @@
 language: java
 dist: trusty
 sudo: true
+services:
+  - docker
 before_cache:
   - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
 cache:
@@ -30,6 +32,7 @@ matrix:
 
 before_install:
   - scripts/install-samtools.sh
+  - scripts/htsget-scripts/start-htsget-test-server.sh
 
 script:
   - if [[ $SPOT_BUGS == "true" ]]; then

build.gradle

@@ -37,6 +37,7 @@ dependencies {
     compile "org.apache.commons:commons-compress:1.19"
     compile 'org.tukaani:xz:1.8'
     compile "gov.nih.nlm.ncbi:ngs-java:2.9.0"
+    compile 'org.sharegov:mjson:1.4.1'
 
     testCompile "org.scala-lang:scala-library:2.12.8"
     testCompile "org.scalatest:scalatest_2.12:3.0.5"

scripts/htsget-scripts/README.md

@@ -0,0 +1,5 @@
+This folder contains scripts and files necessary for starting a local htsget reference server so that htsget functionality can be tested.
+
+`start-htsget-test-server.sh` starts a docker image running the reference server, serving files from the directory `src/test/resources/htsjdk/samtools/BAMFileIndexTest/`.
+
+`htsget_config.json` configures the mapping between path name patterns and resource sources used by the reference server.

scripts/htsget-scripts/htsget_config.json

@@ -0,0 +1,10 @@
+{
+  "readsDataSourceRegistry": {
+    "sources": [
+      {
+        "pattern": "^htsjdk_test\\.(?P<accession>.*)$",
+        "path": "/data/{accession}"
+      }
+    ]
+  }
+}

scripts/htsget-scripts/start-htsget-test-server.sh

@@ -0,0 +1,13 @@
+#!/bin/sh
+
+set -e
+WORKING_DIR=/home/travis/build/samtools/htsjdk
+docker pull ga4gh/htsget-ref:1.1.0
+docker container run -d --name htsget-server -p 3000:3000 --env HTSGET_PORT=3000 --env HTSGET_HOST=http://127.0.0.1:3000 \
+      -v $WORKING_DIR/src/test/resources/htsjdk/samtools/BAMFileIndexTest/:/data \
+      -v $WORKING_DIR/scripts/htsget-scripts:/data/scripts \
+      ga4gh/htsget-ref:1.1.0 \
+      ./htsref -config /data/scripts/htsget_config.json
+docker container ls -a
+
+curl http://localhost:3000

src/main/java/htsjdk/samtools/BAMFileReader.java

@@ -901,27 +901,6 @@ private CloseableIterator<SAMRecord> createStartingAtIndexIterator(final int ref
         return new BAMQueryFilteringIterator(iterator,new BAMStartingAtIteratorFilter(referenceIndex,start));
     }
 
-    /**
-     * @throws java.lang.IllegalArgumentException if the intervals are not optimized
-     * @see QueryInterval#optimizeIntervals(QueryInterval[])
-     */
-    private void assertIntervalsOptimized(final QueryInterval[] intervals) {
-        if (intervals.length == 0) return;
-        for (int i = 1; i < intervals.length; ++i) {
-        final QueryInterval prev = intervals[i-1];
-        final QueryInterval thisInterval = intervals[i];
-            if (prev.compareTo(thisInterval) >= 0) {
-                throw new IllegalArgumentException(String.format("List of intervals is not sorted: %s >= %s", prev, thisInterval));
-            }
-            if (prev.overlaps(thisInterval)) {
-                throw new IllegalArgumentException(String.format("List of intervals is not optimized: %s intersects %s", prev, thisInterval));
-            }
-            if (prev.endsAtStartOf(thisInterval)) {
-                throw new IllegalArgumentException(String.format("List of intervals is not optimized: %s abuts %s", prev, thisInterval));
-            }
-        }
-    }
-
     /**
      * Use the index to determine the chunk boundaries for the required intervals.
      * @param intervals the intervals to restrict reads to
@@ -947,7 +926,7 @@ public static BAMFileSpan getFileSpan(QueryInterval[] intervals, BAMIndex fileIn
     private CloseableIterator<SAMRecord> createIndexIterator(final QueryInterval[] intervals,
                                                              final boolean contained) {
 
-        assertIntervalsOptimized(intervals);
+        QueryInterval.assertIntervalsOptimized(intervals);
 
         BAMFileSpan span = getFileSpan(intervals, getIndex());
 
@@ -971,7 +950,7 @@ public CloseableIterator<SAMRecord> createIndexIterator(final QueryInterval[] in
                                                             final boolean contained,
                                                             final long[] filePointers) {
 
-        assertIntervalsOptimized(intervals);
+        QueryInterval.assertIntervalsOptimized(intervals);
 
         // Create an iterator over the above chunk boundaries.
         final BAMFileIndexIterator iterator = new BAMFileIndexIterator(filePointers);