[med-svn] [stacks] 02/04: Merge tag 'upstream/1.44'

[Andreas Tille]

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tille pushed a commit to branch master
in repository stacks.

commit d1ee70bff5f2985a9915804d67abc8f99ef4720c
Merge: 750b9f1 1d2ea27
Author: Andreas Tille <tille at debian.org>
Date:   Sat Oct 22 21:03:24 2016 +0200

    Merge tag 'upstream/1.44'
    
    Upstream version 1.44

 ChangeLog                 |   20 +
 acinclude.m4              |  583 +++++++++--
 configure                 |  914 ++++++++++++++++-
 configure.ac              |    4 +-
 scripts/load_sequences.pl |    2 +-
 scripts/ref_map.pl        |    5 +-
 src/BamI.h                |  449 +++++----
 src/BamUnalignedI.h       |   89 +-
 src/BowtieI.h             |   19 +-
 src/BustardI.h            |   38 +-
 src/DNANSeq.cc            |  131 +--
 src/DNANSeq.h             |   88 +-
 src/DNASeq.cc             |  328 +++---
 src/DNASeq.h              |   24 +-
 src/FastaI.h              |   40 +-
 src/FastqI.h              |   24 +-
 src/GappedAln.h           |   80 +-
 src/PopMap.h              |    8 +-
 src/PopSum.h              |  122 +--
 src/SamI.h                |  340 ++++---
 src/Tsv.h                 |   20 +-
 src/Vcf.cc                |    2 +-
 src/aln_utils.cc          |   34 +-
 src/bootstrap.h           |  446 ++++-----
 src/catalog_utils.cc      |   40 +-
 src/clean.cc              |  712 ++++++-------
 src/clean.h               |  488 ++++-----
 src/clone_filter.cc       |   96 +-
 src/clone_filter.h        |   16 +-
 src/cmb.cc                |   20 +-
 src/cmb.h                 |    4 +-
 src/constants.h           |   12 +-
 src/cstacks.cc            | 1661 +++++++++++++++---------------
 src/estacks.cc            |  576 +++++------
 src/estacks.h             |    2 +-
 src/export_formats.cc     |  252 ++---
 src/file_io.cc            | 1493 +++++++++++++--------------
 src/file_io.h             |   16 +-
 src/genotypes.cc          | 2448 ++++++++++++++++++++++-----------------------
 src/genotypes.h           |    2 +-
 src/gzFasta.h             |   86 +-
 src/gzFastq.h             |   62 +-
 src/hstacks.cc            |  372 +++----
 src/input.cc              |  215 ++--
 src/input.h               |   31 +-
 src/kmer_filter.cc        | 2134 +++++++++++++++++++--------------------
 src/kmer_filter.h         |    2 +-
 src/kmers.cc              |   70 +-
 src/locus.cc              |   47 +-
 src/locus.h               |   38 +-
 src/log_utils.cc          |    4 +-
 src/models.cc             |  558 +++++------
 src/mst.cc                |   26 +-
 src/mst.h                 |    4 +-
 src/mstack.cc             |   71 +-
 src/ordered.h             |  330 +++---
 src/phasedstacks.cc       | 2010 ++++++++++++++++++-------------------
 src/phasedstacks.h        |  124 +--
 src/populations.cc        |  356 ++++---
 src/process_radtags.cc    | 1509 ++++++++++++++--------------
 src/process_radtags.h     |   30 +-
 src/process_shortreads.cc | 1406 +++++++++++++-------------
 src/process_shortreads.h  |   30 +-
 src/pstacks.cc            |  188 ++--
 src/pstacks.h             |    7 +-
 src/rxstacks.cc           | 2001 ++++++++++++++++++------------------
 src/rxstacks.h            |   10 +-
 src/smoothing.h           |  168 ++--
 src/smoothing_utils.h     |   38 +-
 src/sql_utilities.h       |   22 +-
 src/sstacks.cc            | 1145 ++++++++++-----------
 src/stacks.cc             |    8 +-
 src/stacks.h              |  105 +-
 src/ustacks.cc            |  321 +++---
 src/ustacks.h             |    9 +-
 src/utils.cc              |   96 +-
 src/utils.h               |    4 +-
 src/write.cc              |  268 ++---
 src/write.h               |    2 +-
 79 files changed, 13662 insertions(+), 11893 deletions(-)

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