[med-svn] [circlator] branch upstream updated (03314f4 -> 2224d66)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository circlator.

      from  03314f4   Imported Upstream version 1.4.0
       new  2224d66   New upstream version 1.4.1

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:
 circlator/bamfilter.py                             |  28 +++++-----
 circlator/merge.py                                 |   6 +--
 circlator/tasks/all.py                             |   9 ++--
 circlator/tasks/bam2reads.py                       |   2 +
 circlator/tests/bamfilter_test.py                  |  58 ++++++++++++++++++---
 .../bamfilter_test_run_keep_unmapped.out.reads.fq  |  32 ++++++++++++
 ...test_run.bam => bamfilter_test_run_no_qual.bam} | Bin
 ....bam.bai => bamfilter_test_run_no_qual.bam.bai} | Bin
 .../tests/data/bamfilter_test_run_with_qual.bam    | Bin 0 -> 908 bytes
 ...am.bai => bamfilter_test_run_with_qual.bam.bai} | Bin
 setup.py                                           |   2 +-
 11 files changed, 111 insertions(+), 26 deletions(-)
 create mode 100644 circlator/tests/data/bamfilter_test_run_keep_unmapped.out.reads.fq
 rename circlator/tests/data/{bamfilter_test_run.bam => bamfilter_test_run_no_qual.bam} (100%)
 copy circlator/tests/data/{bamfilter_test_run.bam.bai => bamfilter_test_run_no_qual.bam.bai} (100%)
 create mode 100644 circlator/tests/data/bamfilter_test_run_with_qual.bam
 rename circlator/tests/data/{bamfilter_test_run.bam.bai => bamfilter_test_run_with_qual.bam.bai} (100%)

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