Evaluate empirical splicing status of "perfect" sequencing reads

building

cargo build --release

indexing

./target/release/build_index <input_fasta> <output_index_stem>

This will create 2 files, <output_index_stem>.btex and <output_index_stem>.idx.

mapping / ambiguity determination

./target/release/build_index <index_stem> <fastq_file>

This will write a 2 column output stream to stdout of the form

read_name splicing_status

where read_name is the input record header for each entry in <fastq_file> and splicing_status is one of m, n, a, corresponding to which specific set of targets the read sequence mapped.