[med-svn] [ariba] 02/04: Merge tag 'upstream/2.4.0+ds'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 2b82ba82bd9350983c0c3ded9403d13fd975616c
Merge: 1dcbfdc 784873c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Wed Nov 2 10:47:24 2016 +0100

    Merge tag 'upstream/2.4.0+ds'
    
    Upstream version 2.4.0+ds

 Dockerfile                                         |    2 +-
 README.md                                          |    3 -
 ariba/__init__.py                                  |    2 +-
 ariba/assembly.py                                  |  276 +-
 ariba/assembly_compare.py                          |   17 +-
 ariba/cluster.py                                   |   21 +-
 ariba/clusters.py                                  |    5 +-
 ariba/ext/fml-asm_ariba.cpp                        |  108 +-
 ariba/external_progs.py                            |   38 +-
 ariba/mash.py                                      |   72 -
 ariba/ref_preparer.py                              |    7 +-
 ariba/ref_seq_chooser.py                           |  179 +
 ariba/report.py                                    |    4 +-
 ariba/summary.py                                   |    6 +-
 ariba/tests/assembly_compare_test.py               |    2 +-
 ariba/tests/assembly_test.py                       |  110 +-
 ariba/tests/cluster_test.py                        |   66 +-
 ariba/tests/clusters_test.py                       |    1 -
 .../assembly_assemble_with_fermilite.expected.fa   |   12 +-
 .../assembly_assemble_with_fermilite.expected.log  |   16 +-
 ...mbly_assemble_with_fermilite_fails.expected.log |   16 +-
 .../tests/data/assembly_run_fermilite.expected.fa  |   12 +-
 .../tests/data/assembly_run_fermilite.expected.log |   16 +-
 .../data/assembly_run_fermilite_fails.expected.log |   16 +-
 .../assembly_test_assemble_with_spades_reads_1.fq  |    4 -
 .../assembly_test_assemble_with_spades_reads_2.fq  |    5 -
 .../data/assembly_test_assemble_with_spades_ref.fa |    2 -
 .../assembly_test_check_spades_log_file.log.bad    |    5 -
 .../assembly_test_check_spades_log_file.log.good   |    5 -
 ...est_gapfill_with_gapfiller.scaffolds_no_gaps.fa |  168 -
 ...t_gapfill_with_gapfiller.scaffolds_with_gaps.fa |  168 -
 ...assembly_test_gapfill_with_gapfiller_reads_1.fq | 8000 --------------------
 ...assembly_test_gapfill_with_gapfiller_reads_2.fq | 8000 --------------------
 .../assembly_test_has_gaps_to_fill.has_gaps.fa     |    2 -
 .../data/assembly_test_has_gaps_to_fill.no_gaps.fa |    4 -
 .../data/assembly_test_rename_scaffolds.in.fa      |    6 -
 .../data/assembly_test_rename_scaffolds.out.fa     |    6 -
 .../assembly_test_set_assembly_kmer_reads_1.fq     |   12 -
 .../assembly_test_set_assembly_kmer_reads_2.fq     |   12 -
 ...r_test_full_run_ref_not_in_cluster.all_refs.fa} |    0
 ...er_test_full_run_ref_not_in_cluster.mash.fa.msh |  Bin 2760 -> 0 bytes
 ariba/tests/data/clusters_test_dummy_db.fa.msh     |  Bin 504 -> 0 bytes
 ariba/tests/data/mash_test_run.in.qry.fa           |   10 -
 ariba/tests/data/mash_test_run.in.ref.fa           |   40 -
 ...er_full_run_best_match_is_in_cluster.allrefs.fa |   50 +
 ...ull_run_best_match_is_in_cluster.clusterrefs.fa |   40 +
 ...er_full_run_best_match_is_in_cluster.contigs.fa |   10 +
 ...r_full_run_best_match_not_in_cluster.allrefs.fa |   50 +
 ...ll_run_best_match_not_in_cluster.clusterrefs.fa |   40 +
 ...r_full_run_best_match_not_in_cluster.contigs.fa |   10 +
 ...seq_chooser_full_run_no_nucmer_match.allrefs.fa |    6 +
 ...chooser_full_run_no_nucmer_match.clusterrefs.fa |    6 +
 ...seq_chooser_full_run_no_nucmer_match.contigs.fa |    2 +
 ..._seq_chooser_full_run_not_in_cluster.allrefs.fa |   50 +
 ..._chooser_full_run_not_in_cluster.clusterrefs.fa |   20 +
 ..._seq_chooser_full_run_not_in_cluster.contigs.fa |   10 +
 .../ref_seq_chooser_matching_contig_pieces.coords  |    6 +
 .../ref_seq_chooser_matching_contig_pieces.ctg.fa  |    8 +
 ...ef_seq_chooser_matching_contig_pieces.expect.fa |    7 +
 .../ref_seq_chooser_matching_contig_pieces.ref.fa  |   10 +
 .../ref_seq_chooser_sequence_is_in_fasta_file.fa   |    4 +
 ariba/tests/mash_test.py                           |   21 -
 ariba/tests/ref_preparer_test.py                   |    1 -
 ariba/tests/ref_seq_chooser_test.py                |   84 +
 ariba/tests/summary_test.py                        |   12 +-
 install_dependencies.sh                            |   10 -
 scripts/ariba                                      |    4 +-
 setup.py                                           |    2 +-
 68 files changed, 817 insertions(+), 17102 deletions(-)

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