Amplimap

- renamed output directories to match rule names:
+ `analysis/bam` -> `analysis/bams`
+ `analysis/bam/coverage` -> `analysis/bams/coverages`
+ `analysis/pileup` -> `analysis/pileups`
+ `analysis/pileup` -> `analysis/pileups`
+ `analysis/pileup_snps` -> `analysis/pileups_snps`
+ `analysis/umi_dedup` -> `analysis/bams_umi_dedup`
- added `general: umi_min_consensus_percentage` setting to specify the minimum fraction of reads in a UMI group that have to agree on the consensus
- add separate `pileups_snps` rule to only run SNP pileups
- improved check for missing paths
- fixed crash if config file was present but empty
- removed excessive logging in `stats_alignment` and `attach_tags_from_unmapped`
- improved documentation of config file

- added tutorials
- added rules to check that tools exist in path (and save their version) before trying to run them
- added check for valid coordinates in probe design file
- added check for non-overlapping target regions in targets file
- added support for space-separated SNPs file
- added `_fraction` columns to long pileups
- added config error checks
- added new tests:
+ run with BWA
+ handle UMIs
+ simulate variants
- fixed bugs:
+ error when mate names ended in /1 and /2
+ probe information missing from pileup files
+ fixed crash on errors with exon annotation file
- config changes:
+ added comments to default config to explain each option
+ added `general: use_raw_reads` option (should work with with unmapped bams as well as fastqs)
+ removed `no_probe_data` option (now detected through `use_raw_reads`)
+ moved some options from `general` into `parse_reads`:
* `trim_primers`
* `trim_min_length`
* `quality_trim_threshold`
* `quality_trim_phred_base`
+ changed defaults for `pileup:validate_probe_targets` and `pileup:filter_softclipped` to false
+ changed default variant caller back to Platypus