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Consecutive genes fix #148

Merged
merged 18 commits into from
Nov 1, 2016
Merged

Consecutive genes fix #148

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0d5d8d3
New class ref_seq_chooser
Oct 20, 2016
07a608f
Add ref_seq_chooser
Oct 20, 2016
e0b945e
Remove dict of contigs parameter
Oct 20, 2016
16b0a6f
Use new ref_seq_chooser
Oct 20, 2016
bf758db
Catch when no nucmer matches
Oct 21, 2016
c5190a2
Remove debug print
Oct 21, 2016
bb5fca9
More verbose logging
Oct 21, 2016
5c74e53
Bug fix numeric sort
Oct 21, 2016
3d088f0
Bug fix getting wrong contig name and then key error
Oct 26, 2016
f86c47a
Use two overlap lengths
Oct 27, 2016
173f546
Write all assemblies to fasta instead of choosing one of them
Oct 27, 2016
8026a0f
Use nucmer to choose closest ref sequence
Oct 31, 2016
6fa28d0
Remove dependency on mash
Oct 31, 2016
5a930ba
Remove sspace and gapfiller
Oct 31, 2016
99acc48
Use percent identity of longest match
Nov 1, 2016
7c54eac
Make yes and yes_nonunique the same colour
Nov 1, 2016
13f2de5
Unhide threads option
Nov 1, 2016
ae3b7fb
Version bump 2.4.0
Nov 1, 2016
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -11,7 +11,7 @@ MAINTAINER [email protected]
#
# Install the dependancies
#
RUN apt-get update -qq && apt-get install -y git bowtie2 cd-hit fastaq libc6 libfml0 libgcc1 libminimap0 libstdc++6 mash mummer python3 python3-setuptools python3-dev python3-pysam python3-pymummer python3-dendropy gcc g++ zlib1g-dev
RUN apt-get update -qq && apt-get install -y git bowtie2 cd-hit fastaq libc6 libfml0 libgcc1 libminimap0 libstdc++6 mummer python3 python3-setuptools python3-dev python3-pysam python3-pymummer python3-dendropy gcc g++ zlib1g-dev

#
# Get the latest code from github and install
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3 changes: 0 additions & 3 deletions README.md
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Expand Up @@ -23,7 +23,6 @@ ARIBA has the following dependencies, which need to be installed:
* [Python3][python] version >= 3.3.2
* [Bowtie2][bowtie2] version >= 2.1.0
* [CD-HIT][cdhit] version >= 4.6
* [MASH][mash] version >= 1.0.2
* [MUMmer][mummer] version >= 3.23


Expand Down Expand Up @@ -74,7 +73,6 @@ to the following dependencies.
|----------------|------------------------|---------------------------|
| Bowtie2 | `bowtie2` | `$ARIBA_BOWTIE2` |
| CD-HIT (est) | `cd-hit-est` | `$ARIBA_CDHIT` |
| MASH | `mash` | `$ARIBA_MASH` |


For example, you could specify an exact version of a bowtie2 executable
Expand Down Expand Up @@ -139,7 +137,6 @@ Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/ariba.svg?
[bowtie2]: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
[cdhit]: http://weizhongli-lab.org/cd-hit/
[ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki
[mash]: https://mash.readthedocs.io/en/latest/
[mummer]: http://mummer.sourceforge.net/
[python]: https://www.python.org/

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2 changes: 1 addition & 1 deletion ariba/__init__.py
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Expand Up @@ -23,13 +23,13 @@
'histogram',
'link',
'mapping',
'mash',
'read_filter',
'read_store',
'refdata_query',
'reference_data',
'ref_genes_getter',
'ref_preparer',
'ref_seq_chooser',
'report',
'report_filter',
'scaffold_graph',
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