Abstract Summary Combinatorial barcoding technologies for single-cell nucleotide sequencing, such as split-pool ligation protocols, involve sequential rounds of cell barcoding to uniquely tag individual cells. The rapid adoption of combinatorial barcoding in recent years is due in part to its scalability across cells and samples. However, small shifts in barcode positions within sequencing reads caused by technical artifacts, e.g. during barcode incorporation or synthesis, can impact the accurate assignment of reads to cell barcodes. Existing processing tools typically assume barcodes contain fixed-length nucleotide sequences located at fixed positions within reads, overlooking any positional variability. Consequently, reads containing truncated or mispositioned barcodes are discarded during initial data processing steps leading to significant data loss. To solve this limitation and maximize the retention of sequencing reads from single-cell combinatorial barcoding experiments, we introduce scarecrow. This tool screens a subsample of reads to generate position-specific barcode profiles, which are then used to flexibly identify barcode sequences in each read whilst accounting for positional errors, a phenomenon we refer to as “jitter”. Barcode matches are then prioritized to minimize nucleotide mismatches and the degree of jitter. These initial profiles are subsequently used to extract and error correct barcode combinations in high throughput sequencing libraries. By incorporating jitter into barcode error correction, scarecrow enables greater data recovery and improved downstream single-cell analyses. Scarecrow is fully open access, implemented in Python, and generates output files using standardized sequence file formats for maximal interoperability. A detailed explanation of the scarecrow workflow can be found in the supplementary materials. Availability and implementation Scarecrow is freely available on GitHub https://github.com/MorganResearchLab/scarecrow and Zenodo https://doi.org/10.5281/zenodo.18621784.

We propose a calculus describing compilation and linking in terms of operations on fragments, i.e. compilation units, without reference to their specific contents. We believe this calculus faithfully reflects the situation within modern programming systems. Binary compatibility in Java prescribes conditions under which modification of fragments does not necessitate recompilation of importing fragments. We apply our calculus to formalize binary compatibility, and demonstrate that several interpretations of the language specification are possible, each with different ramifications. We choose a particular interpretation, justify our choice, formulate and prove properties important for language designers and code library developers.

Separate compilation allows the decomposition of programs into units that may be compiled separately, and linked into an executable. Traditionally, separate compilation was equivalent to the compilation of all units together, and modification and re-compilation of one unit required re-compilation of all importing units.Java suggests a more flexible framework, in which the linker checks the integrity of the binaries to be combined. Certain source code modifications, such as addition of methods to classes, are defined as binary compatible. The language description guarantees that binaries of types (i.e. classes or interfaces) modified in binary compatible ways may be re-compiled and linked with the binaries of types that imported and were compiled using the earlier versions of the modified types.However, this is not always the case: some of the changes considered by Java as binary compatible do not guarantee successful linking and execution. In this paper we study the concepts around binary compatibility. We suggest a formalization of the requirement of safe linking and execution without re-compilation, investigate alternatives, demonstrate several of its properties, and propose a more restricted definition of binary compatible changes. Finally, we prove for a substantial subset of Java, that this restricted definition guarantees error-free linking and execution.