- improvements to ngs_plubming.sampling (reservoir sampling + bloom
- fixed XSQ converstion (was broken along the way in the 0.12.x versions).
It should aso work with Python 3.3
- slight changes to the XSQ conversion command line. Read the –help
- new module ngs_plumbing.sampling
- parameter buffering for parsing.open()
- Fixes for Python 3.3 / Python 2.7 (use of io)
- Fixes for Python 3.3 / Python 2.7 compatibility
- New entry SeqQualEntry (with sequence and quality) in
- New module parsing
- Conditional dependency on jinja2
- Deprecate module scons.
- Static definition to speed-up color-space and XSQ-related
- Fixed quality for CSFASTQ file (the quality line was the same as CSFASTA)
- renamed module ‘string’ to ‘ngsp_string’ (dark/ugly corner in Python’s
import system caused issues on some systems)
- added parameter –buffer-size to script xsq-convert
- fixed issue with FASTQ parsing when the quality line starts with ‘@’
- fixed ZeroDivisionError on when converting XSQ files for which there
is close to no data for a given barcode
- added switch –unassigned to xsq-convert to be able to recover
reads with unassigned barcodes
- fixed unwanted trimming of the last kmer when using the functions
- refactored the options for converting XSQ files. Two families of data formats
can be chosen (FASTA-like or FASTQ-like), and for each either colour-space
or base-space data can be obtained.
- add new module colorspace, and new script to perform colorspace conversions
- option to convert XSQ files into CSFASTQ files
- Report OS errors when trying to create missing directories for the XSQ reports
- Handle F5 reads in XSQ files when having paired-end RNASeq data
- _libdna.slicebit2_frombit2bytes() to slice DNA while remaining bitpacked.
- New kmers.poskmerbit2_frombit2_iter().
- Fixed HTML QC report when subdirectories were not existing
(failed to create them)
- QC plots now resized with the window
- Fixed HTML QC report for paired-end runs
- Added parameters maxhead and maxseq to limit the size of the header
and of the sequence when reading FASTAB files (since there are
otherwise no checks while reading binary files).
- Fixed HTML QC report when the target directory is already existing
- ASCII representation of quality values was incorrect for QUAL files.
- When converting XSQ files, libraries are stored inside directories
corresponding to the respective XSQ file names.
- fixed anchor in the HTML quality reports
- fixed relative path for the QC values when the HTML report is not generated
in the current directory (‘.’)
- ASCII representation of quality values was incorrect for XSQ conversion.
SOLiD is using the Sanger scoring, not the illumina one.
- XSQ files can be inconsistent in may ways. Attempt at getting more robust
- new exception fastq.FastqError when problems while parsing FASTQ files
- fixed handling of flag -i for xsq-convert
- functions in _libdna to make the reverse, complement, and reverse complement
while keeping the DNA bit-packed.
- new methods reversed, complemented, and reversecomplemented for the class dna.PackedDNABytes.