distiller 0.3.5 roadmap

[agalitsyna]

I included here only the issues that are either easy small fixes or structural changes that are important and also easy to introduce.

• Support minimap2, bwa aln, bwa mem2 Support of minimap2, bam mem2 and bwa aln #181
• Add short read alignment for reads <25 bp distiller (bwa mem) cannot handle Hi-C data sequenced with 25bp #141
• Add adaptor trimming built-in adaptor trimming #146
• Fix sra-toolkit issue: fastq-dump fails with "This sra toolkit installation has not been configured." when docker is disabled #157
• Fix exhausted suffixes: Bug: split: output file suffixes exhausted #169
• Option to start from bam files: bam files recycling #178

[Phlya]

We discussed adding filters to stats in distiller and @agalitsyna tried something, but in the end we never implemented it... Shall we do it? I propose to add the --filter 'name"expression' arguments to the dedup command, and also --yaml to actually store all the filter outputs?