[med-svn] [qtltools] branch upstream updated (288141d -> f241cdb)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository qtltools.

      from  288141d   Imported Upstream version 1.0+dfsg
       new  f241cdb   New upstream version 1.1+dfsg

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:
 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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