[med-svn] [stacks] branch master updated (750b9f1 -> b7af9c0)

[Andreas Tille]

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tille pushed a change to branch master
in repository stacks.

      from  750b9f1   Fix script executable paths to debian install dir
       new  1d2ea27   New upstream version 1.44
       new  d1ee70b   Merge tag 'upstream/1.44'
       new  91b80e2   New upstream version
       new  b7af9c0   stacks-web Depends: default-mysql-server | mysql-server

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:
 ChangeLog                 |   20 +
 acinclude.m4              |  583 +++++++++--
 configure                 |  914 ++++++++++++++++-
 configure.ac              |    4 +-
 debian/changelog          |    9 +-
 debian/control            |    2 +-
 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 +-
 81 files changed, 13670 insertions(+), 11896 deletions(-)

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