[med-svn] [circlator] branch upstream updated (87a615c -> c559acc)

[Afif Elghraoui]

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

afif pushed a change to branch upstream
in repository circlator.

      from  87a615c   Imported Upstream version 1.1.4
       new  c559acc   Imported Upstream version 1.2.0

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/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 +-
 install_dependencies.sh                            |     6 +-
 scripts/circlator                                  |     2 +
 setup.py                                           |     4 +-
 28 files changed, 20287 insertions(+), 28 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

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