SAM CIGAR Span Reference — Query versus Reference Length (.csv)
Each alignment's CIGAR decomposed into how many query bases and how many reference bases it consumes, with the resulting 1-based reference end. The three records where those numbers differ are the whole reason CIGAR arithmetic is worth testing.
read_id,flag,reverse_strand,cigar,ref_start_1_based,ref_end_1_based,reference_span,query_length,operations
NX_READ_001,0,false,60M,101,160,60,60,6 0 M
NX_READ_002,0,false,10S50M,141,190,50,60,1 0 S 5 0 M
NX_READ_003,0,false,30M2D30M,181,242,62,60,3 0 M 2 D 3 0 M
NX_READ_004,16,true,25M3I32M,221,277,57,60,2 5 M 3 I 3 2 M
NX_READ_005,0,false,20M5I35M,261,315,55,60,2 0 M 5 I 3 5 M
NX_READ_006,16,true,60M,301,360,60,60,6 0 M
Specifications
- Rows
- 6
- Columns
- 9
- Rule
- M/=/X consume both; I/S consume query only; D/N consume reference only
- Records Where Spans Differ
- 3
- Describes
- the paired SAM file
Testing contract
Reference control- Scenario
- Compute the reference span and query length of every CIGAR in the paired SAM file and diff against this table.
- Expected result
- All six rows match, 10S50M consumes 60 query bases but only 50 reference bases, and 30M2D30M consumes 60 query bases against a 62-base reference span.
What is a .csv file?
CSV (Comma-Separated Values) is a plain-text tabular format where rows are lines and fields are separated by commas, with quoting rules for values that contain delimiters, quotes, or newlines. It has no formal type system and depends on encoding and dialect conventions. It is the most portable format for tabular data exchange.
How to use this file
Use an example CSV to test parsers against quoting and embedded-delimiter edge cases, header handling, encoding detection, and import pipelines into databases or spreadsheets.
How to use this file for testing
“SAM CIGAR Span Reference — Query versus Reference Length (.csv)” is a deterministic Novus Examples fixture for Scientific data, Editor testing, Conversion testing. Citation catalogs (BibTeX, RIS), chemistry structures (MDL Molfile, PDB), and gridded binary data (NetCDF, FITS) — for testing reference managers, molecule viewers, and scientific-data loaders.
Documented properties for this file: 6 rows · 9 columns. Compare results against paired or grouped companions on this page when present (clean↔damaged, searchable↔scanned, or format twins) so scores stay reproducible across runs.
Download the file once, keep the path stable in CI or local scripts, and treat the spec table as the contract: dimensions, seeds, field lists, and roles are intentional. Corrupt or invalid samples are labelled as such — expect parsers to fail loudly rather than silently accept them.
Scientific fixtures are small, valid, and fully synthetic — no real organism, patient, sample, or observation. Point your parser or loader at the file and check it reads the documented records, variables, or headers; binary formats ship a readable twin or metadata listing for comparison.
Code examples
import pandas as pd
df = pd.read_csv("cigar-reference.csv")
print(df.head())
print(df.dtypes)Related files
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- csvFASTQ Quality Score Reference — Both Encodings Decoded (.csv)Every twelfth base of the six reads with its Phred score, the ASCII character it takes under both offsets, and the error probability that score implies. It converts a quality-encoding argument into a lookup you can diff.
- fastqFASTQ Reads — Phred+64 Legacy Encoding (.fastq)The identical reads and identical quality scores written with the legacy Phred+64 offset used by older Illumina pipelines. Decode it with the modern offset and every base looks 31 points better than it is, which is a silent quality inflation rather than a parse failure.
- csvGenomic Coordinate Conventions — BED versus GFF3 Side by Side (.csv)Every interval written in both coordinate conventions with its length, which is identical either way. It is the lookup table for the most common bioinformatics off-by-one, and the length column is what proves a conversion did not quietly change an interval's size.
- nwkNewick Tree — Topology Only, No Branch Lengths (.nwk)The identical tree topology with every branch length and support value stripped, which is what a Newick writer produces when the source tree has no lengths. Comparing the two proves a parser distinguishes 'length zero' from 'no length recorded'.
- csvChemistry Fixture Molecule Index (.csv)One row per molecule used across the chemistry fixtures, with formula, molecular weight, SMILES and the atom and bond counts each file should yield. It is the oracle a cheminformatics toolkit can be scored against without needing a second toolkit to generate the answers.
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