[med-svn] [circlator] 03/07: Merge tag 'upstream/1.2.0'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository circlator.

commit 0a8cdfddfcf4993b6162839c7738fb4b5fc037cd
Merge: e2a01b8 c559acc
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Mar 18 01:18:25 2016 -0700

    Merge tag 'upstream/1.2.0'
    
    Upstream version 1.2.0

 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(-)

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