[med-svn] [circlator] branch master updated (9ee5ec6 -> 0e97525)

[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  9ee5ec6   Add README.source explaining the peculiarities of this packaging
       new  e2a01b8   Add d/watch file
       new  c559acc   Imported Upstream version 1.2.0
       new  0a8cdfd   Merge tag 'upstream/1.2.0'
       new  41053fd   Add ITP number and bump version
       new  ccbc1cd   Refresh patches
       new  81c1442   Populate d/copyright
       new  0e97525   Configure autopkgtest

The 7 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/assemble.py                              |    27 +-
 circlator/common.py                                |     2 +-
 circlator/data/test_contigs.fa                     |  4953 +++++++++
 circlator/data/test_for_reads.fa                   | 10001 +++++++++++++++++++
 circlator/data/test_make_data.sh                   |    23 +
 circlator/data/test_reads.fq.gz                    |   Bin 0 -> 3670492 bytes
 circlator/data/test_ref.fa                         |  5001 ++++++++++
 circlator/data/test_ref.fa.fai                     |     1 +
 circlator/external_progs.py                        |     1 -
 circlator/mapping.py                               |    32 +-
 circlator/merge.py                                 |     9 +-
 circlator/tasks/all.py                             |     6 +
 circlator/tasks/assemble.py                        |     4 +
 circlator/tasks/merge.py                           |     4 +
 circlator/tasks/test.py                            |    55 +
 circlator/tests/assemble_test.py                   |    23 +
 .../data/mapping_test_aligned_read_to_read.bam     |   Bin 0 -> 343 bytes
 .../data/mapping_test_aligned_read_to_read.bam.bai |   Bin 0 -> 96 bytes
 .../mapping_test_aligned_read_to_read.reads.fq     |     8 +
 .../data/mapping_test_aligned_read_to_read.ref.fa  |    10 +
 circlator/tests/data/mapping_test_bwa_index.fa     |    20 +
 circlator/tests/data/mapping_test_bwa_mem.reads.fq |    24 +
 circlator/tests/data/mapping_test_bwa_mem.ref.fa   |    20 +
 .../tests/data/mapping_test_bwa_mem.ref.fa.fai     |     2 +
 circlator/tests/mapping_test.py                    |    77 +-
 debian/changelog                                   |     4 +-
 debian/copyright                                   |    14 +-
 debian/patches/bundle-bioassemblyref.patch         |     2 +-
 debian/tests/control                               |     2 +
 debian/watch                                       |    11 +
 install_dependencies.sh                            |     6 +-
 scripts/circlator                                  |     2 +
 setup.py                                           |     4 +-
 33 files changed, 20310 insertions(+), 38 deletions(-)
 create mode 100644 circlator/data/test_contigs.fa
 create mode 100644 circlator/data/test_for_reads.fa
 create mode 100755 circlator/data/test_make_data.sh
 create mode 100644 circlator/data/test_reads.fq.gz
 create mode 100644 circlator/data/test_ref.fa
 create mode 100644 circlator/data/test_ref.fa.fai
 create mode 100644 circlator/tasks/test.py
 create mode 100644 circlator/tests/data/mapping_test_aligned_read_to_read.bam
 create mode 100644 circlator/tests/data/mapping_test_aligned_read_to_read.bam.bai
 create mode 100644 circlator/tests/data/mapping_test_aligned_read_to_read.reads.fq
 create mode 100644 circlator/tests/data/mapping_test_aligned_read_to_read.ref.fa
 create mode 100644 circlator/tests/data/mapping_test_bwa_index.fa
 create mode 100644 circlator/tests/data/mapping_test_bwa_mem.reads.fq
 create mode 100644 circlator/tests/data/mapping_test_bwa_mem.ref.fa
 create mode 100644 circlator/tests/data/mapping_test_bwa_mem.ref.fa.fai
 create mode 100644 debian/tests/control
 create mode 100644 debian/watch

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