Welcome to bamnostic’s documentation!

This documentation site is a work in progress as I continue to hone my reStructuredText skills. All of the module documentation is here, but a more detailed “Getting Started” should be available soon.

Note

CRAM format is not supported at this time.

Contents:

• Installation
  • Through the conda package manager (Anaconda Cloud)
  • Through the Python Package Index (PyPI)
  • Through pip+Github
  • Traditional GitHub clone
• Getting Started
  • Importing bamnostic
  • Loading your BAM file
  • Get the header
  • Data validation through head()
  • Getting the next read
  • Exploring a read
    • Read Name
    • 0-based Start Position (raw, aligned, reference)
    • CIGAR & QUAL Strings
    • Sequence Length (raw, aligned, reference)
    • Nucleotide Sequence
    • Read Flag and Decoded Flag
  • Serial Access
  • Random Access
• Module documentation
  • Core Module (bamnostic.core)
    • Cigar
    • offset_qual()
    • AlignmentFile
    • AlignedSegment
    • unpack_int32()
    • unpack_int32L()
  • Bgzip BAM Format (BGZF) file handlers (bamnostic.bgzf)
    • unpack_gzip_header()
    • unpack_subfields()
    • unpack_gzip_integrity()
    • unpack_bgzf_metaheader()
    • get_block()
    • BgzfReader
    • BgzfWriter
    • unpack_int32()
    • unpack_int32L()
  • Binary Alignment Map (BAM) file handlers (bamnostic.bam)
    • BAMheader
    • BamReader
    • BamWriter
    • unpack_int32()
    • unpack_int32L()
  • BAM Index (BAI) file handler (bamnostic.bai)
    • unpack_chunk()
    • unpack_intervals()
    • unpack_bid_nchunk()
    • unpack_unmapped()
    • RefIdx
    • reg2bin()
    • reg2bins()
    • Bai
    • unpack_int32()
    • unpack_int32L()
  • Coordinate-Sorted Index (CSI) file handler (bamnostic.csi)
    • unpack_chunk()
    • unpack_bid_loffset_nchunk()
    • unpack_unmapped()
    • reg2bin_csi()
    • reg2bins_csi()
    • Csi
    • unpack_int32()
    • unpack_int32L()
  • BAMnostic Utilities (bamnostic.utils)
    • format_warnings()
    • unpack_int32()
    • unpack_int32L()
    • Roi
    • flag_decode()
    • yes_no()
    • parse_region()
    • unpack()
    • make_virtual_offset()
    • split_virtual_offset()
    • LruDict
    • parse_cigar()
    • check_cigar_arg()
    • cigar_changes()
    • md_changes()
    • ref_gen()
    • cigar_alignment()
• Citation and Support
  • Citation
  • Support for BAMnostic

Indices and tables

• Index

• Module Index

• Search Page