CRAM 3.1 seems unsupported

[lucacozzuto]

I tried running the tool on a cram file (format 3.1) and got

  RustQC v0.2.1 (c868466, built 2026-04-09T12:09:14Z)
  Binary: x86-64-v4 (AVX-512) | CPU: AVX-512 AVX2 SSE4.2 POPCNT detected

  Input:       NIST7035_TAAGGCGA.marked.cram
  Annotation:  gencode.v28.annotation.gtf
  Reference:   GRCh38.primary_assembly.genome.fa
  Stranded:    unstranded
  Paired:      true
  CPU Threads: 8
  Output dir:  ./NIST7035_TAAGGCGA

    Parsing GTF annotation...

  Processing NIST7035_TAAGGCGA.marked.cram
[WARN  rustqc::rna::dupradar::counting] Alignment index not found for NIST7035_TAAGGCGA.marked.cram; falling back to single-threaded processing. Create an index w
ith 'samtools index' to enable parallel processing.
[E::cram_next_slice] Slice decode failure
  ✗ error: Failed to process NIST7035_TAAGGCGA.marked.cram: Error reading alignment record: truncated record in SAM/BAM/CRAM file

[ewels]

Is NIST7035_TAAGGCGA.marked.cram a broken download or anything?

[lucacozzuto]

No, it is a normal cram.

[ewels]

Are you able to create a minimal test example CRAM file that I can use to replicate the error?