[med-svn] [stacks] branch upstream updated (df2c72a -> 1d2ea27)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository stacks.

      from  df2c72a   Imported Upstream version 1.42
       new  1d2ea27   New upstream version 1.44

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:
 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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