Interpolate Sam Pl

# 2) Save per-contig coverage blocks for downstream plotting
interpolate_sam.pl \
  alignments.sorted.sam > coverage.blocks.txt

# 3) Inspect the first region header and counts
interpolate_sam.pl \
  alignments.sorted.sam | head -n 40

Recommended Workflow

1. Start from a SAM file that is already sorted in the order expected by the script.
2. Confirm the reference names and CIGAR strings match the assumptions documented in the source comments.
3. Generate the interpolated count output, then inspect the #RNAME block headers and early counts for sanity.
4. Use the output as a lightweight diagnostic or plotting input rather than as a drop-in replacement for modern pileup/depth tools.

Guardrails

• This script expects a SAM filename as its first positional argument; --help and --version are treated as missing-file names and error out.
• The input SAM must be sorted.
• It expects simple CIGAR operations (M, I, and D) and a colon-delimited RNAME format such as chromosome:NCBI36:18:1:76117153:1.
• The source comments note an MAQ-specific assumption that flag 0x0010 marks the second read in paired-end data, so validate behavior before using it on arbitrary modern SAM files.