Read Counting

Counts properly paired reads within the KIV-2 VNTR region for each sample, filtered by mapping quality and SAM flag as specified in the config.

grid.utils.count_reads.count_reads(config, console=None)
grid.utils.count_reads.count_reads_in_region(cram_file, ref_fasta, chrom, start, end, proper_flags, min_mapq=1)

Count properly paired reads in a genomic region using pysam.

Parameters:

  • cram_file (str)

  • ref_fasta (str)

  • chrom (str)

  • start (int)

  • end (int)

  • proper_flags (set[int])

  • min_mapq (int)

Return type:

int

grid.utils.count_reads.process_single_cram(path, ref_fasta, chrom, start, end, proper_flags, min_mapq=1, console=None)

Process a single sequence alignment file and count reads in region.

Parameters:

  • path (str) – Path to sequence alignment file

  • ref_fasta (str) – Path to reference genome FASTA

  • chrom (str) – Chromosome name

  • start (int) – Start position

  • end (int) – End position

  • proper_flags (set[int]) – Set of SAM flags to count

  • min_mapq (int)

Returns:

Read count or “Error”

Return type:

int or str

grid.utils.count_reads.write_read_results(output_file, basename, count, write_lock)

Write a single result to the output file in a thread-safe manner.

Parameters:

  • output_file (Path) – Path to output file

  • basename (str) – Sample basename

  • count (int | str) – Read count or “Error”

  • write_lock (allocate_lock) – Threading lock for safe file writing

Return type:

None