[med-svn] [circlator] branch master updated (4065b8c -> 8d37990)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository circlator.

      from  4065b8c   Add explicit build-dependency on bwa with proper minimum version
       new  03b0ae8   Imported Upstream version 1.2.1
       new  25f2238   Merge tag 'upstream/1.2.1'
       new  10dd112   Refresh patches
       new  b0ac069   Don't restrict pysam max version
       new  793b9ac   Update minimum dependency versions
       new  8d37990   Prepare new revision

The 6 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:
 circlator/__init__.py                      |  9 +++++++
 circlator/bamfilter.py                     | 20 ++++++++++++++-
 circlator/common.py                        |  2 --
 circlator/external_progs.py                | 10 +++-----
 circlator/tasks/all.py                     | 23 +++++++++++++++--
 circlator/tasks/bam2reads.py               |  2 ++
 circlator/tasks/progcheck.py               |  5 ++--
 circlator/tasks/version.py                 |  3 ++-
 circlator/versions.py                      | 40 ++++++++++++++++++++++++++++++
 debian/changelog                           | 10 ++++++++
 debian/control                             |  4 +--
 debian/patches/bundle-bioassemblyref.patch |  6 ++---
 debian/patches/pysam-maxversion.patch      | 17 +++++++++++++
 debian/patches/series                      |  1 +
 debian/patches/spades-call.patch           |  2 +-
 setup.py                                   |  8 +++---
 16 files changed, 137 insertions(+), 25 deletions(-)
 create mode 100644 circlator/versions.py
 create mode 100644 debian/patches/pysam-maxversion.patch

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