[med-svn] [jellyfish1] 03/03: Merge tag 'upstream/1.1.11'

[Andreas Tille]

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tille pushed a commit to branch master
in repository jellyfish1.

commit c220063191457d8d0244155209c556aef38c8b2b
Merge: 97751ec 379377e
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 20 09:40:28 2017 +0200

    Merge tag 'upstream/1.1.11'
    
    Upstream version 1.1.11

 Makefile.am                                        |   144 +-
 Makefile.in                                        |  1259 +-
 aclocal.m4                                         |   106 +-
 config.guess                                       |   449 +-
 config.h.in                                        |     9 +
 config.sub                                         |   227 +-
 configure                                          | 16036 +++++++++----------
 configure.ac                                       |    30 +-
 depcomp                                            |   190 +-
 gtest.mk                                           |    13 +-
 install-sh                                         |    29 +-
 jellyfish-1.1.pc.in                                |     2 +-
 jellyfish/allocators_malloc.hpp                    |     2 +-
 jellyfish/allocators_mmap.hpp                      |     2 +-
 jellyfish/allocators_shm.hpp                       |     2 +-
 jellyfish/capped_integer.hpp                       |     6 +-
 jellyfish/circular_buffer.hpp                      |     2 +-
 jellyfish/cite.cc                                  |     3 +-
 jellyfish/compacted_hash.hpp                       |    88 +-
 jellyfish/concurrent_queues.hpp                    |   203 +-
 jellyfish/count_main_cmdline.hpp                   |   363 +-
 jellyfish/dbg.cc                                   |     7 +
 jellyfish/dbg.hpp                                  |     2 +-
 jellyfish/direct_indexing_array.hpp                |     6 +-
 jellyfish/direct_sorted_dumper.hpp                 |    22 +-
 jellyfish/divisor.hpp                              |   144 +-
 jellyfish/dna_codes.hpp                            |    20 +-
 jellyfish/double_fifo_input.hpp                    |     2 +-
 jellyfish/dump_main.cc                             |    53 +-
 jellyfish/dumper.hpp                               |    25 +-
 jellyfish/err.hpp                                  |    41 +-
 jellyfish/fastq_dumper.hpp                         |     2 +-
 jellyfish/file_parser.cc                           |     4 +-
 jellyfish/floats.hpp                               |    13 +-
 jellyfish/generate_sequence.cc                     |     2 +-
 jellyfish/half.h                                   |     2 +-
 jellyfish/hash.hpp                                 |    13 +-
 jellyfish/hash_fastq_merge.cc                      |     2 +-
 jellyfish/hash_merge.cc                            |     2 +-
 jellyfish/heap.hpp                                 |     4 +-
 jellyfish/invertible_hash_array.hpp                |   167 +-
 jellyfish/locking_hash_counters.hpp                |     4 +-
 jellyfish/locks_pthread.hpp                        |     6 +-
 jellyfish/mapped_file.hpp                          |     6 +-
 jellyfish/mer_counter.cc                           |    58 +-
 jellyfish/misc.cc                                  |    13 +
 jellyfish/misc.hpp                                 |     2 +
 jellyfish/offsets_key_value.hpp                    |    68 +-
 jellyfish/parse_dna.hpp                            |     2 +-
 jellyfish/parse_qual_dna.hpp                       |     4 +-
 jellyfish/parse_read.hpp                           |     8 +-
 jellyfish/randomc.h                                |     4 +-
 jellyfish/raw_dumper.hpp                           |    26 +-
 jellyfish/simple_circular_buffer.hpp               |   134 +
 jellyfish/simple_growing_array.hpp                 |     2 +-
 jellyfish/sorted_dumper.hpp                        |    43 +-
 jellyfish/square_binary_matrix.cc                  |    18 +-
 jellyfish/square_binary_matrix.hpp                 |    15 +-
 jellyfish/test_double_fifo_input.cc                |     2 +-
 jellyfish/time.hpp                                 |     6 +-
 jellyfish/yaggo.hpp                                |     4 +-
 ltmain.sh                                          |  4017 +++--
 m4/gnulib-cache.m4                                 |    35 -
 m4/libtool.m4                                      |  2248 ++-
 m4/ltoptions.m4                                    |    32 +-
 m4/ltversion.m4                                    |    12 +-
 m4/lt~obsolete.m4                                  |    12 +-
 missing                                            |    53 +-
 tests/compat.sh.in                                 |     2 +-
 tests/parallel_direct_indexing.sh                  |    23 +-
 tests/parallel_fastq_direct_indexing.sh            |    28 +
 tests/parallel_fastq_hashing.sh                    |    16 +-
 tests/parallel_hashing.sh                          |    37 +-
 .../gtest/include/gtest/internal/gtest-internal.h  |    10 +
 .../gtest/include/gtest/internal/gtest-port.h      |    10 +
 .../gtest/include/gtest/internal/gtest-string.h    |    10 +
 unit_tests/gtest/src/gtest-port.cc                 |     6 +
 unit_tests/test_offsets_key_value.cc               |   288 +-
 unit_tests/test_simple_circular_buffer.cc          |    71 +
 unit_tests/test_square_binary_matrix.cc            |   133 +
 unit_tests/unit_tests.sh                           |     2 +-
 81 files changed, 14813 insertions(+), 12355 deletions(-)

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