[med-svn] [staden-io-lib] branch upstream updated (97e9a05 -> 445eda3)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository staden-io-lib.

      from  97e9a05   New upstream version 1.14.8
       new  445eda3   New upstream version 1.14.9

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
been added to this reference.


Summary of changes:
 CHANGES                         |    72 +
 ChangeLog                       | 11048 --------------------------------------
 Makefile.am                     |     5 +-
 Makefile.in                     |   432 +-
 README => README.md             |    97 +-
 aclocal.m4                      |   758 +--
 bootstrap                       |     2 +-
 config.guess                    |   184 +-
 config.sub                      |   106 +-
 configure                       |   661 +--
 configure.in                    |    11 +-
 depcomp                         |   487 +-
 install-sh                      |    14 +-
 io_lib/Makefile.am              |     4 +-
 io_lib/Makefile.in              |   667 +--
 io_lib/bam.c                    |   178 +-
 io_lib/bam.h                    |    18 +-
 io_lib/bgzip.c                  |   466 ++
 io_lib/{binning.h => bgzip.h}   |    38 +-
 io_lib/cram_codecs.c            |   109 +
 io_lib/cram_codecs.h            |    13 +
 io_lib/cram_decode.c            |   112 +-
 io_lib/cram_encode.c            |    26 +-
 io_lib/cram_io.c                |    97 +-
 io_lib/cram_io.h                |     4 +-
 io_lib/cram_stats.c             |     9 +-
 io_lib/cram_structs.h           |    13 +-
 io_lib/crc32.c                  |     2 +
 io_lib/dstring.c                |    19 +-
 io_lib/hash_table.h             |     1 +
 io_lib/rANS_static.c            |   413 +-
 io_lib/sam_header.c             |    70 +-
 io_lib/sam_header.h             |     4 +
 io_lib/scram.c                  |    37 +
 io_lib/scram.h                  |    16 +
 io_lib/srf.c                    |    22 +-
 io_lib/zfio.c                   |    41 +-
 io_lib_config.h                 |    21 +-
 io_lib_config.h.in              |    11 +-
 ltmain.sh                       |     4 +-
 man/man1/scramble.1             |     5 +
 missing                         |   414 +-
 progs/Makefile.am               |     5 +-
 progs/Makefile.in               |   411 +-
 progs/cram_filter.c             |   919 ++++
 progs/scram_flagstat.c          |     7 +-
 progs/scramble.c                |    65 +-
 test-driver                     |   139 -
 tests/Makefile.am               |     8 +
 tests/Makefile.in               |   679 +--
 tests/data/aux#aux.dz           |   Bin 95 -> 0 bytes
 tests/data/tr                   |  7453 -------------------------
 tests/data/xx#large_aux.cram    |   Bin 22668 -> 0 bytes
 tests/data/xx#supplementary.sam |    10 -
 54 files changed, 4385 insertions(+), 22022 deletions(-)
 delete mode 100644 ChangeLog
 rename README => README.md (65%)
 create mode 100644 io_lib/bgzip.c
 copy io_lib/{binning.h => bgzip.h} (66%)
 create mode 100644 progs/cram_filter.c
 delete mode 100755 test-driver
 delete mode 100644 tests/data/aux#aux.dz
 delete mode 100644 tests/data/tr
 delete mode 100644 tests/data/xx#large_aux.cram
 delete mode 100644 tests/data/xx#supplementary.sam

-- 
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