Changelog.txt

[1.0.13]
> Fixed alleles plot when common alleles contain 'N'

[1.0.12]
> Added --max_paired_end_reads_overlap for FLASH merging step

[1.0.11]
> CRISPRessoPooled looks for cleaned/slugified names (produced by CRISPResso) for combining pools.
> Fixed a Warning: invalid value encountered in double_scalars  y_label_values=np.arange(0,y_max,y_max/6.0)
> Fixed a problem with Pandas #ILovePandas where if a subset returns a single
row, it returns a scalar instead of a DataFrame.  This resulted in an
error: ERROR: ("'numpy.int64' object is not iterable", u'occurred at index 0')

[1.0.10]
> Fixed bug in CRISPResso when writing the Quantification_of_editing_frequency.txt file. 'nan's in the np.sum cause the writing to fail, resulting in no output.

[1.0.9]
> Implemented parameter 'bowtie2_options_string' in CRISPRessoPooled for changing parameters passed to bowtie2
> Added debug functionality to print most common unaligned reads in cases
where less than half of reads align in CRISPRessoPooled

[1.0.8]
> Fixed the cup!
> Fixed  allels around cut site plot with seaborn >= 0.8.0
> Added the option --allow-outies to flash to also try combining read pairs in the "outie" orientation
[1.0.7]
> Alleles around cut sites fixed if multiple cuts are present

[1.0.6]
> Fixed plots when more than 2 sgRNA sequences are provided
> Introduced new summary table for alleles around each cut site
> Introduced a new graphical report for allele around each cut site (Figures files starting with 9.)

[1.0.5]
> Fixed small error in saving offset for cut sites in plots

[1.0.4]
> Fixed quantification of insertion in reads that align in the reverse complement of the amplicon
> Fixed window not symmetric for w=1
> Fixed cut point visualization if the guide is in the reverse amplicon


[1.0.3]
> Introduced a new utility: CRISPRessoCount to count guides representation given a fastq or fastq.gz file

[1.0.2]
> Fixed function that removed characters not allowed  forcing the name to become lowercase and causing problem with CRISPRessoPooled

[1.0.1]
> Fixed -s parameter being ignored if -q was not specified
> Remove characters not allowed in the name if specified with the --name option (they are all replaced with '_')
> New option --split_paired_end to support paired end reads encoded in a single file (for example data obtained trough the MGH core in Boston: )

[1.0.0] First stable release!
> Introduced a new report in output: allelic frequency table (Alleles_frequency_table.txt). Table with a summary of all the alleles detected, % of reads supporting them and
classification (unmodified, NHEJ, HDR and mixed). You can open this file with Excel.