Commits · 2c2df4e098463682ba4755f61fec09ba06ded98f · OBITools / OBITools3 · GitLab

17 Oct, 2018 11 commits
- C: Added a trick to suppress compilation warnings about an unused · 2c2df4e0
  Celine Mercier authored Oct 17, 2018
```
function actually called in a macro
```
  2c2df4e0
- Updated prototypes with no arguments with a void argument as suggested · 8ce6dd6d
  Celine Mercier authored Oct 17, 2018
```
by compilation warnings
```
  8ce6dd6d
- New command: obi export · df700863
  Celine Mercier authored Oct 17, 2018
  
  df700863
- Cython: Added fasta and fastq writers · 32d8396e
  Celine Mercier authored Oct 17, 2018
  
  32d8396e
- Cython: minor fixes · 6a8670d2
  Celine Mercier authored Oct 17, 2018
  
  6a8670d2
- Cython: obi stats fixed to work with reworked options (forgotten in a · ec73fa84
  Celine Mercier authored Oct 17, 2018
```
previous commit)
```
  ec73fa84
- Cython: Sequence objects: Quality strings are now returned as bytes · 11032ec9
  Celine Mercier authored Oct 17, 2018
```
instead of str
```
  11032ec9
- Cython: Added Column line methods to get a Column line as a str or · 8a9ba8b0
  Celine Mercier authored Oct 17, 2018
```
bytes, and elements (keys, values) with None values are not returned
anymore
```
  8a9ba8b0
- Cython: updated the URI decoding to handle outputs other than DMS · 135d3b6e
  Celine Mercier authored Oct 17, 2018
  
  135d3b6e
- Cython: rearranged input and output format options to have both and · 58589e04
  Celine Mercier authored Oct 17, 2018
```
updated commands accordingly
```
  58589e04
- Cython: fasta and fastq parsers now return bytes and take NA string · e6bbe13d
  Celine Mercier authored Oct 17, 2018
```
argument
```
  e6bbe13d
09 Oct, 2018 3 commits
- Cython: fastq formatter · 61b00d60
  Celine Mercier authored Oct 09, 2018
  
  61b00d60
- Cython: fasta and fastq header formatter · 8029493c
  Celine Mercier authored Oct 09, 2018
  
  8029493c
- Cython: fasta writer · aa5ee534
  Celine Mercier authored Oct 09, 2018
  
  aa5ee534
07 Oct, 2018 13 commits
- New command: obi history to print DMS or view history in bash, dot or · e31c8ea5
  Celine Mercier authored Oct 07, 2018
```
ascii formats
```
  e31c8ea5
- obi test: updated to test comments · 9e700ddc
  Celine Mercier authored Oct 07, 2018
  
  9e700ddc
- Commands: updated for JSON formatted comments with history · e9a41c5b
  Celine Mercier authored Oct 07, 2018
  
  e9a41c5b
- Cython: DMS: JSON formatted comments and history handling · 35cf2962
  Celine Mercier authored Oct 07, 2018
  
  35cf2962
- Cython: Views: JSON formatted comments and history handling · 74be3c39
  Celine Mercier authored Oct 07, 2018
  
  74be3c39
- Cython: Columns: goes with handling of JSON formatted comments · c6ee0bad
  Celine Mercier authored Oct 07, 2018
  
  c6ee0bad
- Cython utils: functions convert to bytes or str and to remove all empty · ffd5bc76
  Celine Mercier authored Oct 07, 2018
```
objects from a complex object
```
  ffd5bc76
- Cython: Columns: added support for JSON formatted comments · 704d9b04
  Celine Mercier authored Oct 07, 2018
  
  704d9b04
- Views: implemented handling of JSON formatted comments · 86bb582a
  Celine Mercier authored Oct 07, 2018
  
  86bb582a
- Columns: implemented handling of JSON formatted comments · bc8c3940
  Celine Mercier authored Oct 07, 2018
  
  bc8c3940
- Obierrno: added errno for JSON related errors · cef458f5
  Celine Mercier authored Oct 07, 2018
  
  cef458f5
- DMS: implemented full information file with JSON formatted comments · 2736a926
  Celine Mercier authored Oct 07, 2018
  
  2736a926
- C library to handle JSON formatted comments using the cJSON library · 79f41857
  Celine Mercier authored Oct 07, 2018
  
  79f41857
14 Aug, 2018 2 commits
- obi grep: added all the missing filtering options · 1b6b6d82
  Celine Mercier authored Aug 14, 2018
  
  1b6b6d82
- Taxonomy Cython API: added is_ancestor() function · 3847850a
  Celine Mercier authored Aug 14, 2018
  
  3847850a
13 Aug, 2018 1 commit
- New command: obi stats · b57e938c
  Celine Mercier authored Aug 13, 2018
  
  b57e938c
10 Aug, 2018 3 commits
- Minor fixes · 2dc7fcce
  Celine Mercier authored Aug 10, 2018
  
  2dc7fcce
- New command: obi tail · e096b929
  Celine Mercier authored Aug 10, 2018
  
  e096b929
- New command: obi head · 2c634dae
  Celine Mercier authored Aug 10, 2018
  
  2c634dae
09 Aug, 2018 1 commit
- New command: obi sort · 7a4cdc0c
  Celine Mercier authored Aug 09, 2018
  
  7a4cdc0c
08 Aug, 2018 4 commits
- Commands: ngsfilter and alignpairedend can now be used in whichever · e8dc5eb1
  Celine Mercier authored Aug 08, 2018
```
order
```
  e8dc5eb1
- More explicit predicate error when checking that sequences and qualities · 3fcf29a7
  Celine Mercier authored Aug 08, 2018
```
match
```
  3fcf29a7
- Cython API: more explicit "Can't guess type" exception · 080a97cc
  Celine Mercier authored Aug 08, 2018
  
  080a97cc
- Cython API: the associated sequence column for a quality column can now · 9c9aec25
  Celine Mercier authored Aug 08, 2018
```
be specified at the Python level
```
  9c9aec25
28 Jul, 2018 2 commits
- Cython: embl file parser · 303648bd
  Celine Mercier authored Jul 28, 2018
  
  303648bd
- New command: obi ecopcr · 2ba6d161
  Celine Mercier authored Jul 28, 2018
  
  2ba6d161