JAL-2909 recognise .bam extension in URL and allow location spec as suffix - e.g...

[jalview.git] / src / jalview / io / BamFile.java

diff --git a/src/jalview/io/BamFile.java b/src/jalview/io/BamFile.java
index c8bac62..8a04867 100644 (file)
--- a/src/jalview/io/BamFile.java
+++ b/src/jalview/io/BamFile.java
@@ -21,20 +21,24 @@
 package jalview.io;
 
 import jalview.datamodel.CigarParser;
+import jalview.datamodel.Range;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 import java.util.PrimitiveIterator.OfInt;
 import java.util.SortedMap;
 
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMRecordIterator;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.SamInputResource;
 import htsjdk.samtools.SamReader;
 import htsjdk.samtools.SamReaderFactory;
 import htsjdk.samtools.ValidationStringency;
@@ -94,13 +98,24 @@ public class BamFile extends AlignFile
   public BamFile(FileParse source) throws IOException
   {
     super(true, source);
+    parseSuffix();
     final SamReaderFactory factory = SamReaderFactory.makeDefault()
             .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
                     SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
             .validationStringency(ValidationStringency.SILENT);
 
     // File-based bam
-    fileReader = factory.open(source.inFile);
+    if (source.getDataSourceType() == DataSourceType.FILE)
+    {
+      fileReader = factory.open(source.inFile);
+    }
+    else
+    {
+      // locate index ?
+      String index = source.getDataName() + ".bai";
+      fileReader = factory.open(SamInputResource.of(source.getDataName())
+              .index(new URL(index)));
+    }
   }
   
   @Override
@@ -187,5 +202,39 @@ public class BamFile extends AlignFile
     chromosome = chr;
     start = s;
     end = e;
+    suffix = chromosome + ":" + start + "-" + end;
+  }
+
+  public boolean parseSuffix()
+  {
+    if (suffix == null)
+    {
+      return false;
+    }
+    int csep = suffix.indexOf(":");
+    int rsep = suffix.indexOf("-", csep);
+    if (csep < 0 || rsep < 0 || suffix.length() - rsep <= 1)
+    {
+      return false;
+    }
+    String chr, p1, p2;
+    chr = suffix.substring(0, csep);
+    p1 = suffix.substring(csep + 1, rsep);
+    p2 = suffix.substring(rsep + 1);
+    int cstart, cend;
+    try
+    {
+      cstart = Integer.parseInt(p1);
+      cend = Integer.parseInt(p2);
+    } catch (Exception e)
+    {
+      warningMessage = (warningMessage == null ? "" : warningMessage + "\n")
+              + "Couldn't parse range from " + suffix;
+      return false;
+    }
+    chromosome = chr;
+    start = cstart;
+    end = cend;
+    return true;
   }
 }