Commits · 8ce6dd6d1a95963c1adab3b521f1d50109cae7e6 · OBITools / OBITools3 · GitLab

17 Oct, 2018 10 commits
- Updated prototypes with no arguments with a void argument as suggested · 8ce6dd6d
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by compilation warnings
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  Celine Mercier committed Oct 17, 2018
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- New command: obi export · df700863
  Celine Mercier committed Oct 17, 2018
  
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- Cython: Added fasta and fastq writers · 32d8396e
  Celine Mercier committed Oct 17, 2018
  
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- Cython: minor fixes · 6a8670d2
  Celine Mercier committed Oct 17, 2018
  
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- Cython: obi stats fixed to work with reworked options (forgotten in a · ec73fa84
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previous commit)
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  Celine Mercier committed Oct 17, 2018
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- Cython: Sequence objects: Quality strings are now returned as bytes · 11032ec9
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instead of str
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  Celine Mercier committed Oct 17, 2018
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- Cython: Added Column line methods to get a Column line as a str or · 8a9ba8b0
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bytes, and elements (keys, values) with None values are not returned
anymore
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  Celine Mercier committed Oct 17, 2018
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- Cython: updated the URI decoding to handle outputs other than DMS · 135d3b6e
  Celine Mercier committed Oct 17, 2018
  
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- Cython: rearranged input and output format options to have both and · 58589e04
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updated commands accordingly
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  Celine Mercier committed Oct 17, 2018
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- Cython: fasta and fastq parsers now return bytes and take NA string · e6bbe13d
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argument
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  Celine Mercier committed Oct 17, 2018
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09 Oct, 2018 3 commits
- Cython: fastq formatter · 61b00d60
  Celine Mercier committed Oct 09, 2018
  
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- Cython: fasta and fastq header formatter · 8029493c
  Celine Mercier committed Oct 09, 2018
  
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- Cython: fasta writer · aa5ee534
  Celine Mercier committed Oct 09, 2018
  
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07 Oct, 2018 13 commits
- New command: obi history to print DMS or view history in bash, dot or · e31c8ea5
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ascii formats
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  Celine Mercier committed Oct 07, 2018
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- obi test: updated to test comments · 9e700ddc
  Celine Mercier committed Oct 07, 2018
  
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- Commands: updated for JSON formatted comments with history · e9a41c5b
  Celine Mercier committed Oct 07, 2018
  
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- Cython: DMS: JSON formatted comments and history handling · 35cf2962
  Celine Mercier committed Oct 07, 2018
  
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- Cython: Views: JSON formatted comments and history handling · 74be3c39
  Celine Mercier committed Oct 07, 2018
  
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- Cython: Columns: goes with handling of JSON formatted comments · c6ee0bad
  Celine Mercier committed Oct 07, 2018
  
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- Cython utils: functions convert to bytes or str and to remove all empty · ffd5bc76
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objects from a complex object
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  Celine Mercier committed Oct 07, 2018
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- Cython: Columns: added support for JSON formatted comments · 704d9b04
  Celine Mercier committed Oct 07, 2018
  
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- Views: implemented handling of JSON formatted comments · 86bb582a
  Celine Mercier committed Oct 07, 2018
  
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- Columns: implemented handling of JSON formatted comments · bc8c3940
  Celine Mercier committed Oct 07, 2018
  
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- Obierrno: added errno for JSON related errors · cef458f5
  Celine Mercier committed Oct 07, 2018
  
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- DMS: implemented full information file with JSON formatted comments · 2736a926
  Celine Mercier committed Oct 07, 2018
  
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- C library to handle JSON formatted comments using the cJSON library · 79f41857
  Celine Mercier committed Oct 07, 2018
  
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14 Aug, 2018 2 commits
- obi grep: added all the missing filtering options · 1b6b6d82
  Celine Mercier committed Aug 14, 2018
  
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- Taxonomy Cython API: added is_ancestor() function · 3847850a
  Celine Mercier committed Aug 14, 2018
  
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13 Aug, 2018 1 commit
- New command: obi stats · b57e938c
  Celine Mercier committed Aug 13, 2018
  
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10 Aug, 2018 3 commits
- Minor fixes · 2dc7fcce
  Celine Mercier committed Aug 10, 2018
  
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- New command: obi tail · e096b929
  Celine Mercier committed Aug 10, 2018
  
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- New command: obi head · 2c634dae
  Celine Mercier committed Aug 10, 2018
  
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09 Aug, 2018 1 commit
- New command: obi sort · 7a4cdc0c
  Celine Mercier committed Aug 09, 2018
  
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08 Aug, 2018 4 commits
- Commands: ngsfilter and alignpairedend can now be used in whichever · e8dc5eb1
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order
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  Celine Mercier committed Aug 08, 2018
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- More explicit predicate error when checking that sequences and qualities · 3fcf29a7
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match
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  Celine Mercier committed Aug 08, 2018
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- Cython API: more explicit "Can't guess type" exception · 080a97cc
  Celine Mercier committed Aug 08, 2018
  
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- Cython API: the associated sequence column for a quality column can now · 9c9aec25
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be specified at the Python level
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  Celine Mercier committed Aug 08, 2018
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28 Jul, 2018 3 commits
- Cython: embl file parser · 303648bd
  Celine Mercier committed Jul 28, 2018
  
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- New command: obi ecopcr · 2ba6d161
  Celine Mercier committed Jul 28, 2018
  
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- Cython: fixed a bug when reading an uncompressed file in binary mode · 275d85dc
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where the first 4 characters would not be read
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  Celine Mercier committed Jul 28, 2018
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