[med-svn] [beagle] branch master updated (851b415 -> 22e50df)

[Dylan Aïssi]

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

      from  851b415   Finalize changelog
       new  2d9f148   Remove embedded htsjdk
       new  7ef25aa   Imported Upstream version 4.1~160222-8ef+dfsg
       new  2341009   Merge tag 'upstream/4.1_160222-8ef+dfsg'
       new  22e50df   Remove PDF

The 4 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:
 debian/changelog                                   |   4 +-
 debian/control                                     |   2 +-
 debian/copyright                                   |  57 +-
 debian/doc-base                                    |   6 -
 debian/patches/01_Update_to_htslib.patch           |  27 +
 debian/patches/series                              |   1 +
 debian/rules                                       |  12 +-
 debian/source/include-binaries                     |   1 -
 debian/upstream.docs/beagle_4.1_09Feb16.pdf        | Bin 657091 -> 0 bytes
 debian/watch                                       |   3 +-
 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 --------------
 29 files changed, 39 insertions(+), 3176 deletions(-)
 delete mode 100644 debian/doc-base
 create mode 100644 debian/patches/01_Update_to_htslib.patch
 create mode 100644 debian/patches/series
 delete mode 100644 debian/source/include-binaries
 delete mode 100644 debian/upstream.docs/beagle_4.1_09Feb16.pdf
 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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