Code

Minimise files#74

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martinghunt merged 25 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:minimise_filesmartinghunt/ariba:minimise_filesCopy head branch name to clipboardMay 3, 2016

+343-123

Commits

Commits on Apr 29, 2016

• Start writing ReadStore, new method _sort_file

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  b3d00f8

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• Add read_store

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  c1128a5

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• New method _compress_and_index_file

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  a73a986

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• sort and compress in __init__

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  8fc3dcb

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• New method get_reads

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  5ae61dc

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• remove one import pysam (was there twice)

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  1dc4745

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• New method clean

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  b9808be

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• Make input files if root_dir does not exist

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  39a20f5

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• Protect against overwriting infile

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  b8fafa0

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• Make read store file instead of fastq files for each cluster

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  a43c7ee

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• Use read store in each cluster

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  c58a855

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• Write message when getting reads

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  40ed0fc

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• Add missing @ in fastq file name lines

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  1032409

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• Add missing test file

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  c41b05c

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• Pass clean option

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  97d66e6

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• extract reads and references in run(), not __init__()

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  7176e80

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Commits on May 3, 2016

• Store assembled ref seqs in memory instead writing to file

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  a842008

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• Fix function call to use new syntax

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  cf08815

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• Get assembled seqs from memory, not files

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  70f43db

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• Typo in log message

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  5d5868b

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• Delete read store files

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  727e61a

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• gzip assembled seqs fasta file

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  b59c19d

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• Delete cluster dir asap

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  bf7d9bb

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• Remove self.log_fh (breaks multithreading)

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  d3bee7a

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• Pass clean option when multithreading

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  4d3ea9d

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