Add ten ALT records
Edit ten additional eligible BAM alignment records. If the input already contains three ALT reads, the output aims for thirteen.
target_mode = added_alt_reads
Local engine · research use only
Add a defined number of ALT-supporting alignment records, keep molecular families coherent, and verify every changed record before the output is published.
Python 3.10+ · Windows, macOS, Linux · no runtime dependencies · BAMs stay on your computer
chr7:55,249,071 C>T
A precise question deserves a precise control
Edit ten additional eligible BAM alignment records. If the input already contains three ALT reads, the output aims for thirteen.
target_mode = added_alt_reads
Measure the baseline first, then edit only what is needed. Three existing ALT reads means seven additional edits.
target_mode = final_alt_reads
Retain the original VAF workflow when a proportion, rather than a record count, is the intended control.
target_mode = vaf
Try the count logic
This illustrates count semantics. The real preflight also considers eligibility and molecular-family sizes.
Designed for real sequencing files
A hosted page cannot safely browse arbitrary BAM paths on a colleague’s hard drive. SpikeForge therefore uses a browser interface backed by a loopback-only engine on the same computer as the data.
Code, launcher, examples, tests, and documentation.
Single BAM, no-write preflight, and validated batch CSV.
Private candidate, verification, atomic output, truth package.
Verification is a gate, not a badge
$ survey chr1:500 A>T › requested added_alt_reads = 10 › planned 10 records · exact feasible › rewrite private candidate BAM › verify in=3,270 out=3,270 ✓ identical 3,260 ✓ modified 10 expected records ✓ unexpected 0 PASS atomic publication completed
Count targeting, transaction behavior, truth fields, batch parsing, server APIs, verifier and realism regressions.
The pre-existing BAM, FASTQ, fusion, indexing, batch, and reproducibility registry remains green.
Bamnostic independently parsed all 3,270 output records and measured exactly ten new ALT bases.
Bamnostic loaded the generated index and fetched the edited interval from an official HTSlib fixture-derived output.
Audit trail included
.bamModified alignment file.bam.baiIndex for coordinate-sorted inputtruth.vcfRequested, baseline, planned, achieved, and exactness fieldsedit_ledger.tsvOne row per record-level editplanted_read_names.tsvRecord identities and digestsmanifest.jsonConfiguration, checksums, audit and verification outcomeScientific boundaries
BAM editing tests processing from the aligned-read stage. It does not test extraction, library preparation, sequencing, or alignment. Use FASTQ controls through the production aligner for full-pipeline experiments.
A BAM alignment record is not automatically a unique DNA molecule. SpikeForge preserves mate, UMI, and duplicate-family coherence; exact small counts can therefore be infeasible.
Run the intended samtools/Picard stack, caller, filters, and visual review on representative outputs. A modeled or synthetic result is not clinical sensitivity or clinical validation.
Research preview 1.1.0rc1
Download one complete ZIP. On Windows, extract it and double-click Launch SpikeForge.cmd. The package includes the source, wheel, examples, test suite, and biologist quick start.