Change logs

version 0.13.0:

• improvements to ngs_plubming.sampling (reservoir sampling + bloom filter)
• 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

version 0.12.4:

• new module ngs_plumbing.sampling

version 0.12.3:

• parameter buffering for parsing.open()

version 0.12.2

• Fixes for Python 3.3 / Python 2.7 (use of io)

version 0.12.1

• Fixes for Python 3.3 / Python 2.7 compatibility

version 0.12.0

• New entry SeqQualEntry (with sequence and quality) in fastq
• New module parsing
• Conditional dependency on jinja2
• Deprecate module scons.

version 0.11.1

• Fixed tests

version 0.11.0

• Licenses
• Static definition to speed-up color-space and XSQ-related data extraction

version 0.10.1

• Fixed quality for CSFASTQ file (the quality line was the same as CSFASTA)

version 0.10.0

• 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

version 0.9.1

• fixed unwanted trimming of the last kmer when using the functions kmers.kmerbytes_frombit2_iter(), kmers.kmerbit2_frombit2_iter(), poskmers.kmerbit2_frombit2_iter()

version 0.9.0

• 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

version 0.8.2

• option to convert XSQ files into CSFASTQ files

version 0.8.1

• 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

version 0.8.0

• _libdna.slicebit2_frombit2bytes() to slice DNA while remaining bitpacked.
• New kmers.poskmerbit2_frombit2_iter().

version 0.7.6

• Fixed HTML QC report when subdirectories were not existing (failed to create them)
• QC plots now resized with the window

version 0.7.5

• 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

version 0.7.4

• 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 (‘.’)

version 0.7.3

• ASCII representation of quality values was incorrect for XSQ conversion. SOLiD is using the Sanger scoring, not the illumina one.

version 0.7.2

• XSQ files can be inconsistent in may ways. Attempt at getting more robust against that

version 0.7.1

• new exception fastq.FastqError when problems while parsing FASTQ files
• fixed handling of flag -i for xsq-convert

version 0.7.0

• 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.