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CHANGELOG
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CHANGELOG
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v0.4.1 - 08/01/18
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Check return code from KMC and SPAdes and raise error if not 0.
v0.4.0 - 30/11/17
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Allow nontrait kmer thresholds to be set independently
v0.3.5 - 13/07/17
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Remove nonword characters from complex config files sample names.
v0.3.4 - 12/06/17
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Dont generate the Kmer plot by default, takes to much RAM
v0.3.3 - 12/05/17
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Allow a maximum contig coverage to be set.
v0.3.2 - 12/05/17
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Lower default values
v0.3.1 - 10/05/17
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Allow user to choose if both reads need to be present to filter them.
v0.3.0 - 09/05/17
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Require forward and reverse reads to contain a trait kmer.
v0.2.3 - 05/05/17
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Check spades assembly was successful.
v0.2.2 - 04/05/17
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Fix y axes in kmer plot.
v0.2.1 - 04/05/17
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Extend parallelism to other parts of the method.
v0.2.0 - 03/05/17
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Use GNU parallel.
v0.1.13 - 03/05/17
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Abandon multiprocessing due to memory errors.
v0.1.12 - 02/05/17
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FASTA files should always have a kmer filter of 1.
v0.1.11 - 02/05/17
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Bug fix for memory leak in when using multiple processes.
v0.1.10 - 28/04/17
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Parallelise initial database generation and filtering.
v0.1.9 - 28/04/17
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Bug fix to make plot kmers work with KMC 2.3.0.
v0.1.8 - 28/04/17
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Allow for dashes in the filenames.
v0.1.7 - 27/04/17
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Support for using FASTA files as input.
v0.1.6 - 21/04/17
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Add a script to plot the kmers.
v0.1.5 - 17/02/17
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Skip assembly step if all the data is filtered out.
v0.1.4 - 14/02/17
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Check SPAdes directories before deleting.
v0.1.3 - 13/02/17
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Allow for careful flag to be used with SPAdes.
v0.1.2 - 1/02/17
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Allow for low coverage contigs to be filtered out.
v0.1.1 - 31/01/17
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Increase default min contig length to be about 4 times the average fragment size.
Reduce the default kmer size to 51.
v0.1.0 - 31/01/17
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Rescaffold at the end by extracting kmers from spades assembly, reextracting reads, and reassembling & filtering.
v0.0.3 - 18/01/17
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Cleanup SPAdes output files to reduce the amount of disk space used.
The final output is now the scaffolded assembly rather than the contigs.
Improve documentation.
v0.0.2 - 16/01/17
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Allow for the trait kmers to be filtered differently. By default all kmers in the trait set only get used for filtering reads for assembly (union). This can be changed to strict so only kmers occuring in all trait samples are used (intersection).
Validate input values.
Allow for a max number of kmers filter.
v0.0.1 - 12/01/17
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Initial version.