Spladder

bugfix release - correcting use of cram input in sparse mode

Bugfix release
- move to numpy and remove deprecation warnings
- address 115 and 122
- address parsing problem when input bam files and have the form *bam.bam

This release has the following changes:

* improved handling of CRAM input files
* fixing a bug leading to truncated sample names in distributed quantification

This release adds experimental support for CRAM files and updates some dependencies.

This release has the following changes:
* event IDs in text output are now more consistent (e.g., what previously was exon_skip.1 in gff and exon_skip_1 in txt output, now is consistently exon_skip.1)
* a command for the external chunked merge of many splicing graphs has been introduced (allowing for better distribution of large cohorts)
* some typos were fixed

This release introduces a new visualisation mode

* splicing graphs, events, coverage, etc can now be visualised with individual tracks
* documentation was extended to describe new visualisation mode
* a bug that caused `--validate-sg` to be ignored was fixed
* a new feature to specific the support for edges in `--validate-sg` was added