Prepping for clip
logging with logger instead of print
refactor
revs to misowrap for combining miso_bf files
Adding options for defining what counts as constitutive exon
Combining miso comparisons into one file
Combining miso comparisons into one file
Adding duplicates postprocessing to CLIP
fastx utils
Collapsing fastq files for CLIP
Proper quality filter flag for Illumina FASTQ files when calling fastx_collapser
Sorting BED file
Producing BEDs from regions in addition to GFF, flushing GFF buffer to avoid truncated GFFs [bugfix]
Using tagBam to map reads to regions, outputting 3p and 5p UTRs during init
Fraction of reads in each region of QC regions
QC sketches
QC sketches
QC revs
Fixed init to output region BED files with transcript ID rather than gene ID, to allow transcript-centered statistics to be computed
Storing cumulative QC region lengths and lengths by coordinates