Maple

Bamtagmultiome

• Now verifies if a bam index is available and creates one if it's not available
• Continues without a reference when it is not indexed
• Fixed cluster jobs, the resulting read groups are now correct and all contigs including alternative contigs are all processed.
• Added script to estimate mappability for digest protocols, and this file can be supplied to bamtagmultiome to filter for map ability.
• Added write_program_tag method to write provenance information to bam, this is used by bamtagmultiome to add the arguments used for generating the file.

Additions

Created a lot of API documentation, for example for Fragment

Added FourThiouridine (4su) class and analysis script for newly synthesized RNA.

Added function sorted_bam_file to write straight to a sorted and indexed bam file

Updates

The QC fail bit of reads is set when the associated fragment is not valid.

MoleculeIterator is now much faster when reading through regions with very high coverage.

MoleculeIterator can now read from an iterable yielding single end reads

BAM Sorting is now performed in local directory with uuid4 prefix to prevent flooding /tmp

Added deprecation warning to universalBamTagger.py

demux.py does not allow paths with a star in it anymore.