Update to version 1.3.1

[EricKutschera]

• Add gene_id to gtf output
• Adjust version checks and allow more recent nhmmer versions
• Handle 'X' and '=' cigar operations
• Fix bug when Q step is run with minimal arguments
• Handle secondary alignments
• Update how reads are split for C steps
• Improve error message when chr from alignment is not found in reference fasta
• Fix off-by-1 error in gtf output
• Add automated tests
• Improve thread error checking
• Add sorting to get deterministic novel isoform IDs
• Use the split .fasta in the C step
• Update expected example output
• Use TMPDIR in S step in snakemake
• Update parsing for new version of snakemake
• Suppress error message if git commit not found
• Handle reused slurm IDs
• Increase default Q step memory