[med-svn] [beagle] branch upstream updated (486aca4 -> 7ef25aa)

[Dylan Aïssi]

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bob.dybian-guest pushed a change to branch upstream
in repository beagle.

      from  486aca4   Imported Upstream version 4.1~160222-8ef
       new  7ef25aa   Imported Upstream version 4.1~160222-8ef+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 net/sf/samtools/Defaults.java                      |  49 --
 net/sf/samtools/FileTruncatedException.java        |  46 --
 net/sf/samtools/SAMException.java                  |  44 --
 net/sf/samtools/SAMFormatException.java            |  44 --
 net/sf/samtools/util/BinaryCodec.java              | 662 ---------------------
 .../util/BlockCompressedFilePointerUtil.java       | 101 ----
 .../samtools/util/BlockCompressedInputStream.java  | 484 ---------------
 .../samtools/util/BlockCompressedOutputStream.java | 312 ----------
 .../util/BlockCompressedStreamConstants.java       | 118 ----
 net/sf/samtools/util/BlockGunzipper.java           | 115 ----
 net/sf/samtools/util/HttpUtils.java                | 102 ----
 net/sf/samtools/util/IOUtil.java                   | 124 ----
 net/sf/samtools/util/RuntimeEOFException.java      |  46 --
 net/sf/samtools/util/RuntimeIOException.java       |  46 --
 net/sf/samtools/util/SeekableBufferedStream.java   |  90 ---
 net/sf/samtools/util/SeekableFileStream.java       |  69 ---
 net/sf/samtools/util/SeekableHTTPStream.java       | 153 -----
 net/sf/samtools/util/SeekableStream.java           |  37 --
 net/sf/samtools/util/StringUtil.java               | 460 --------------
 19 files changed, 3102 deletions(-)
 delete mode 100644 net/sf/samtools/Defaults.java
 delete mode 100644 net/sf/samtools/FileTruncatedException.java
 delete mode 100644 net/sf/samtools/SAMException.java
 delete mode 100644 net/sf/samtools/SAMFormatException.java
 delete mode 100644 net/sf/samtools/util/BinaryCodec.java
 delete mode 100644 net/sf/samtools/util/BlockCompressedFilePointerUtil.java
 delete mode 100644 net/sf/samtools/util/BlockCompressedInputStream.java
 delete mode 100644 net/sf/samtools/util/BlockCompressedOutputStream.java
 delete mode 100644 net/sf/samtools/util/BlockCompressedStreamConstants.java
 delete mode 100644 net/sf/samtools/util/BlockGunzipper.java
 delete mode 100644 net/sf/samtools/util/HttpUtils.java
 delete mode 100644 net/sf/samtools/util/IOUtil.java
 delete mode 100644 net/sf/samtools/util/RuntimeEOFException.java
 delete mode 100644 net/sf/samtools/util/RuntimeIOException.java
 delete mode 100644 net/sf/samtools/util/SeekableBufferedStream.java
 delete mode 100644 net/sf/samtools/util/SeekableFileStream.java
 delete mode 100644 net/sf/samtools/util/SeekableHTTPStream.java
 delete mode 100644 net/sf/samtools/util/SeekableStream.java
 delete mode 100644 net/sf/samtools/util/StringUtil.java

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