[med-svn] [ariba] branch upstream updated (4c36268 -> 784873c)
Sascha Steinbiss
satta at debian.org
Wed Nov 2 09:57:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository ariba.
from 4c36268 New upstream version 2.3.0+ds
new 784873c New upstream version 2.4.0+ds
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:
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(-)
delete mode 100644 ariba/mash.py
create mode 100644 ariba/ref_seq_chooser.py
delete mode 100644 ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq
delete mode 100644 ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq
delete mode 100644 ariba/tests/data/assembly_test_assemble_with_spades_ref.fa
delete mode 100644 ariba/tests/data/assembly_test_check_spades_log_file.log.bad
delete mode 100644 ariba/tests/data/assembly_test_check_spades_log_file.log.good
delete mode 100644 ariba/tests/data/assembly_test_gapfill_with_gapfiller.scaffolds_no_gaps.fa
delete mode 100644 ariba/tests/data/assembly_test_gapfill_with_gapfiller.scaffolds_with_gaps.fa
delete mode 100644 ariba/tests/data/assembly_test_gapfill_with_gapfiller_reads_1.fq
delete mode 100644 ariba/tests/data/assembly_test_gapfill_with_gapfiller_reads_2.fq
delete mode 100644 ariba/tests/data/assembly_test_has_gaps_to_fill.has_gaps.fa
delete mode 100644 ariba/tests/data/assembly_test_has_gaps_to_fill.no_gaps.fa
delete mode 100644 ariba/tests/data/assembly_test_rename_scaffolds.in.fa
delete mode 100644 ariba/tests/data/assembly_test_rename_scaffolds.out.fa
delete mode 100644 ariba/tests/data/assembly_test_set_assembly_kmer_reads_1.fq
delete mode 100644 ariba/tests/data/assembly_test_set_assembly_kmer_reads_2.fq
rename ariba/tests/data/{cluster_test_full_run_ref_not_in_cluster.mash.fa => cluster_test_full_run_ref_not_in_cluster.all_refs.fa} (100%)
delete mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa.msh
delete mode 100644 ariba/tests/data/clusters_test_dummy_db.fa.msh
delete mode 100644 ariba/tests/data/mash_test_run.in.qry.fa
delete mode 100644 ariba/tests/data/mash_test_run.in.ref.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords
create mode 100644 ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa
create mode 100644 ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa
delete mode 100644 ariba/tests/mash_test.py
create mode 100644 ariba/tests/ref_seq_chooser_test.py
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