[med-svn] [fastqc] 01/03: Path to samtools changed when switching from libsam-java to libhtsjdk-java

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastqc.

commit fbc845aabc0757ce002395368ff2c012ec232da1
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jan 14 15:11:09 2016 +0100

    Path to samtools changed when switching from libsam-java to libhtsjdk-java
---
 debian/patches/adapt_to_htslib.patch | 25 +++++++++++++++++++++++++
 debian/patches/series                |  1 +
 2 files changed, 26 insertions(+)

diff --git a/debian/patches/adapt_to_htslib.patch b/debian/patches/adapt_to_htslib.patch
new file mode 100644
index 0000000..c97c5ea
--- /dev/null
+++ b/debian/patches/adapt_to_htslib.patch
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 14 Jan 2016 13:50:56 +0100
+Bug-Debian: https://bugs.debian.org/810843
+Description: Path to samtools changed when switching from libsam-java
+ to libhtsjdk-java
+
+--- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java
++++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java
+@@ -25,11 +25,11 @@ import java.io.IOException;
+ import java.util.Iterator;
+ import java.util.List;
+ 
+-import net.sf.samtools.CigarElement;
+-import net.sf.samtools.CigarOperator;
+-import net.sf.samtools.SAMFileReader;
+-import net.sf.samtools.SAMFormatException;
+-import net.sf.samtools.SAMRecord;
++import htsjdk.samtools.CigarElement;
++import htsjdk.samtools.CigarOperator;
++import htsjdk.samtools.SAMFileReader;
++import htsjdk.samtools.SAMFormatException;
++import htsjdk.samtools.SAMRecord;
+ 
+ public class BAMFile implements SequenceFile {
+ 
diff --git a/debian/patches/series b/debian/patches/series
index ca9e6da..0801e7d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ build_xml.patch
 fastqc.patch
 fix-help-call.patch
 set_configuration_path.patch
+adapt_to_htslib.patch

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