Coral plot: IndexError

[zhober]

When running coral plot with Coral 2.0, I encountered the error IndexError: list index out of range. No output files were generated in the specified output directory.
The command executed was:

coral plot --ref hg38 --bam /home/qukungroup/zhober/workspace/nanopore/guppy/${sample}/guppy.sorted.bam \
        --graph ./coral/amplicon1_cycles.txt --cycle-file ./coral/amplicon1_cycles.txt --output-prefix ./plot/${sample} \
        --region None --plot-graph --plot-cycles --num-cycles 1

I also noticed that some command help documentation does not match the descriptions in the GitHub README.md file. For example, in coral plot, the --regionand --num-cycles parameters are listed as 'Required arguments', and I also had to include these parameters to run the command successfully. Could you consider making these two parameters 'Optional arguments' instead?

This is the help documentation of coral plot:

(coral) zhober@hanhai22-01:~/workspace/nanopore/script$ coral plot --help
                                                                                                                                                                                                                                                             
 Usage: coral plot [OPTIONS]                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                             
 Generate plots of amplicon cycles and/or graph from AA-formatted output files                                                                                                                                                                               
                                                                                                                                                                                                                                                             
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *  --ref                                            TEXT      Reference genome. [default: None] [required]                                                                                                                                                │
│ *  --graph                                          FILENAME  AmpliconSuite-formatted *.graph file. [default: None] [required]                                                                                                                            │
│ *  --cycle-file                                     FILENAME  AmpliconSuite-formatted cycles file. [default: None] [required]                                                                                                                             │
│ *  --bam                                            PATH      Sorted indexed (long read) bam file. [default: None] [required]                                                                                                                             │
│ *  --output-prefix                                  TEXT      Prefix of output files. [default: None] [required]                                                                                                                                          │
│ *  --num-cycles                                     INTEGER   Only plot the first NUM_CYCLES cycles. [default: None] [required]                                                                                                                           │
│ *  --region                                         TEXT      Specifically visualize only this region, argument formatted as 'chr1:pos1-pos2'. [default: None] [required]                                                                                 │
│    --plot-graph           --no-plot-graph                     Visualize breakpoint graph. [default: no-plot-graph]                                                                                                                                        │
│    --plot-cycles          --no-plot-cycles                    Visualize (selected) cycles. [default: no-plot-cycles]                                                                                                                                      │
│    --only-cyclic-paths    --no-only-cyclic-paths              Only plot cyclic paths from cycles file. [default: no-only-cyclic-paths]                                                                                                                    │
│    --max-coverage                                   FLOAT     Limit the maximum visualized coverage in the graph. [default: inf]                                                                                                                          │
│    --min-mapq                                       FLOAT     Minimum mapping quality to count read in coverage plotting. [default: 0.0]                                                                                                                  │
│    --gene-subset-list                               TEXT      List of genes to visualize (will show all by default).                                                                                                                                      │
│    --hide-genes           --no-hide-genes                     Do not show gene track. [default: no-hide-genes]                                                                                                                                            │
│    --gene-fontsize                                  FLOAT     Change size of gene font. [default: 12.0]                                                                                                                                                   │
│    --bushman-genes        --no-bushman-genes                  Reduce gene set to the Bushman cancer-related gene set. [default: no-bushman-genes]                                                                                                         │
│    --help                                                     Show this message and exit.                                                                                                                                                                 │
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