[med-svn] [Git][med-team/igv][master] adapt to htsjdk in debian

[Olivier Sallou]

Olivier Sallou pushed to branch master at Debian Med / igv


Commits:
f0d97f61 by Olivier Sallou at 2018-10-18T10:14:24Z
adapt to htsjdk in debian

- - - - -


1 changed file:

- debian/patches/fix_gradle.patch


Changes:

=====================================
debian/patches/fix_gradle.patch
=====================================
@@ -115,3 +115,40 @@ Forwarded: no
 -    requires swing.layout;
 +    requires swing.layout.debian;
  }
+--- a/src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
++++ b/src/main/java/org/broad/igv/util/stream/IGVSeekableBufferedStream.java
+@@ -88,27 +88,6 @@
+         return actualSkip;
+     }
+ 
+-    @Override
+-    public synchronized void reset() throws IOException {
+-
+-        if (markpos < 0) {
+-            throw new IOException("Resetting to invalid mark");
+-        }
+-        position = markpos;
+-
+-    }
+-
+-    @Override
+-    public synchronized void mark(int readlimit) {
+-        this.markpos = (int) position;
+-        this.marklimit = readlimit;
+-    }
+-
+-    @Override
+-    public boolean markSupported() {
+-        return true;
+-    }
+-
+     public void seek(final long position) throws IOException {
+         this.position = position;
+     }
+@@ -227,4 +206,4 @@
+             bufferSize = tmpBufferSize;
+         }
+     }
+-}
+\ No newline at end of file
++}



View it on GitLab: https://salsa.debian.org/med-team/igv/commit/f0d97f61b1333a680bcf8b69700b9906ae2c4edd

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View it on GitLab: https://salsa.debian.org/med-team/igv/commit/f0d97f61b1333a680bcf8b69700b9906ae2c4edd
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