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Commits on Dec 9, 2015

• fix of MRO for GZipMixin and reversion of file to _file

  Chris7

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• GZipMixin class that adds a check if a file type object passed in is gzip

  Chris7

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Commits on Dec 2, 2015

• Version 1.9.1

  marcelm

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• Helpful error message when --too-short/long-paired-output not given

  marcelm

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• Changelog for 1.9.1

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• Test --too-short-output without --too-short-paired-output

  marcelm

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Commits on Nov 25, 2015

• Fix #156: Add --too-short-paired-output and --too-long-paired-output options

  marcelm

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Commits on Nov 23, 2015

• Explain read-pair filtering and --pair-filter option

  marcelm

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• Rearrange help further

  marcelm

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• Shuffle help: Show read modification options before filtering options.

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  marcelm

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Commits on Nov 21, 2015

• Forgot to add some test files

  marcelm

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Commits on Nov 20, 2015

• Add --pair-filter option

  marcelm

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• Simplify by getting rid of the trimmed_and_untrimmed_writers function

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  marcelm

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• Rename AdapterMatch to Match

  marcelm

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• match_to docstring

  marcelm

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• Use AdapterCutter.with_adapters in report

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  marcelm

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• Rename reads_matched to with_adapters

  marcelm

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• Remove debugging output

  marcelm

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• Move AdapterCutter to modifiers module

  marcelm

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• make parse_braces a function instead of static method

  marcelm

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• Factor out generate_adapter_name

  marcelm

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• Fix wrong grammar

  marcelm

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• Docstring for modifiers module

  marcelm

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• v2.0.dev0

  marcelm

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Commits on Nov 16, 2015

• Print out also the affected line if FASTQ is malformed

  marcelm

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Commits on Nov 7, 2015

• no cover pragmas

  marcelm

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Commits on Oct 29, 2015

• Also test on Python 3.5

  marcelm

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• Version 1.9

  marcelm

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• Reduce minimum overlap if it is too large.

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  marcelm

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Commits on Oct 27, 2015

• Changelog

  marcelm

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• --discard-trimmed did not work as expected in paired-end mode

  marcelm

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Commits on Oct 21, 2015

• Anchored 5' adapters can now be specified by writing '-a SEQUENCE...'

  marcelm

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• Refactor: Use boolean flags instead of the "degenerate" bit field

  marcelm

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• Document some ideas for how to specify adapters

  marcelm

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Commits on Oct 8, 2015

• Changelog

  marcelm

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