`--sampling-frac` issues in v0.6.1

[SuhasSrinivasan]

As discussed, creating an issue to track observed behavior and changes.

Documentation Issue

The below error message lacks information about the link between --sampling-frac and --seed.

Expected Behavior
The error message and command-line help text should explicitly state the dependency between --seed and --sampling-frac. Specifically, the documentation should clarify that --seed is only valid when used in conjunction with --sampling-frac. If a user provides --seed without --sampling-frac, the error message should clearly explain this relationship rather than just stating that a required argument is missing.

error: the following required arguments were not provided:
  --sampling-frac <SAMPLING_FRAC>

Usage: modkit pileup --reference <REFERENCE_FASTA> --sampling-frac <SAMPLING_FRAC> --modified-bases <MODIFIED_BASES>... --threads <THREADS> --seed <SEED> --mod-threshold <MOD_THRESHOLDS> <IN_BAM> <OUT_BED>

Using sampling fraction stalls the process

After an hour, confirming that the below did not work for v0.6.1, stalled at the sampling stage.

THREADS=8

            "${MODKIT_PATH}" pileup \
            --modified-bases C:m A:a A:17596 T:17802 \
                --threads "${THREADS}" \
                --reference "${REFERENCE_PATH}" \
                --sampling-frac 0.0005 \
                --seed 1234567 \
                --mod-threshold "a:${MOD_THRESHOLD}" \
                --mod-threshold "m:${MOD_THRESHOLD}" \
                --mod-threshold "17802:${MOD_THRESHOLD}" \
                --mod-threshold "17596:${MOD_THRESHOLD}" \
                "${bam_sorted}" "${pile_file}"

> parsed user-input threshold 0.5 for mod-code 17596
> parsed user-input threshold 0.5 for mod-code 17802
> parsed user-input threshold 0.5 for mod-code a
> parsed user-input threshold 0.5 for mod-code m
> discarded 223943 contigs with zero aligned reads
> parsed 4 base modification(s). Base modifications other than 'A:17596,A:a,C:m,T:17802' will be counted as 'N_other'.
> adding single-base motif: 'A 0'
> adding single-base motif: 'C 0'
> adding single-base motif: 'T 0'
> sampling 0.05% of reads
^C