Class CramComparison

java.lang.Object
htsjdk.samtools.cram.CramComparison
public class CramComparison extends Object
Command-line tool for comparing two SAM/BAM/CRAM files record-by-record. Handles known CRAM/SAM differences (auto-generated MD/NM, unsigned B-array types) and reports mismatches with clear field-level detail.

Exit codes: 0 = comparison completed (match or mismatch), 2 = error.

  • Constructor Details

    • CramComparison

      public CramComparison()

  • Method Details

    • main

      public static void main(String[] args)

    • run

      public static int run(String[] args)
      Run the comparison and return the exit code (0=match, 1=mismatch, 2=error). Separated from main() for testability.