[med-svn] [qtltools] 02/06: Merge tag 'upstream/1.1+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository qtltools.

commit 81fa5fe33ef37475aa4b5faa5462dc8bc82abadd
Merge: 0b70e0f f241cdb
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jan 16 10:04:58 2017 +0100

    Merge tag 'upstream/1.1+dfsg'
    
    Upstream version 1.1+dfsg

 Makefile                                     | 81 +++++----------------------
 README                                       |  2 +-
 lib/OTools/otools.h                          |  6 +-
 src/QTLtools.cpp                             |  8 ++-
 src/common/data.h                            |  2 +-
 src/mode_cis/cis_chunking.cpp                |  4 ++
 src/mode_cis/cis_data.h                      |  2 +
 src/mode_cis/cis_initilization.cpp           |  1 +
 src/mode_cis/cis_main.cpp                    | 21 ++++++-
 src/mode_cis/cis_permutation_pass.cpp        |  4 +-
 src/mode_cis/cis_read_phenotypes.cpp         |  9 ++-
 src/mode_correct/correct_data.h              |  8 ++-
 src/mode_correct/correct_main.cpp            |  9 ++-
 src/mode_correct/correct_management.cpp      |  8 ---
 src/mode_correct/correct_processing.cpp      | 34 +++++++++++-
 src/mode_correct/correct_read_covariates.cpp | 81 +++++++++++++++++++++++++++
 src/mode_fdensity/fdensity_process.cpp       | 36 ++++++++++--
 src/mode_fenrich/fenrich_management.cpp      | 11 +++-
 src/mode_match/match_process.cpp             |  7 ++-
 src/mode_quan/quan_chunking.cpp              | 19 ++++++-
 src/mode_quan/quan_data.h                    |  8 +--
 src/mode_quan/quan_main.cpp                  | 22 +++++++-
 src/mode_quan/quan_printResults.cpp          |  2 +
 src/mode_quan/quan_readBAM.cpp               | 83 +++++++++++++++++-----------
 src/mode_rtc/rtc_common.cpp                  |  2 +-
 src/mode_trans/trans_chunking.cpp            | 18 +++++-
 26 files changed, 339 insertions(+), 149 deletions(-)

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