Region targets

[esteinig]

• add target regions logic using minimap2-rs
• add support for specifying targets in config - deserialize into struct
• deprecate sam mapping logic - not using dorado fork
• test previous human chromosome targets that change to logic still works
• add file input for lists of targets
• renamed target struct "name" field to "reference" in config.rs and added optional "name" field for target region specification to better keep track of which e.g. gene is targeted
• add better log message to experiment input
• test target file input
• test on a single chromosome run
• add evaluation and coverage plots for regions

Target file format (tab-delimited), no header, can be mixed formats:

1. Single field with reference name (sequence name present in index) (no target coordinates)
2. Target coordinates on reference sequence, fields:
   • reference (sequence name present in index)
   • start (1-based, closed)
   • end (1-based, closed)
   • name (assigned name of target sequence)

When specified in TOML config list (targets) can also be mixed formats:

1. reference (no target coordinates)
2. {reference}::{start}::{end}::{name} (1-based, closed)

Region alignment logic must consider:

• Start inside target range: alignment start >= target range start and alignment start <= target range end
• End inside target range: alignment end >= target range start and alignment end <= target range end
• Spans target range: alignment start <= target range start and alignment end >= target range end

Modified evaluation scripts:

• separate alignment with minimap2 and paf output
• consideration of secondary alignment logic as in decision logic for unblocking
• rework to always consider target file with optional regions - specifies a target with start=0 and end=0 to be considered mapped if the target reference matches (naive / broad cases for targeted sequencing) as previously implemented without coordinates - in the unblock decision logic this is considered as optional start end values of target specifications in config