biobambam: tools for read pair collation based algorithms on BAM files

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. In this paper we introduce biobambam, an API for efficient BAM file reading supporting the efficient collation of alignments by read name without performing a complete resorting of the input file and some tools based on this API performing tasks like marking duplicate reads and conversion to the FastQ format. In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities in the Picard suite the approach of biobambam can often perform an equivalent task more efficiently in terms of the required main memory and run-time.Comment: 17 pages, 3 figures, 2 table

A study of systems implementation languages for the POCCNET system

The results are presented of a study of systems implementation languages for the Payload Operations Control Center Network (POCCNET). Criteria are developed for evaluating the languages, and fifteen existing languages are evaluated on the basis of these criteria

libcppa - Designing an Actor Semantic for C++11

Parallel hardware makes concurrency mandatory for efficient program execution. However, writing concurrent software is both challenging and error-prone. C++11 provides standard facilities for multiprogramming, such as atomic operations with acquire/release semantics and RAII mutex locking, but these primitives remain too low-level. Using them both correctly and efficiently still requires expert knowledge and hand-crafting. The actor model replaces implicit communication by sharing with an explicit message passing mechanism. It applies to concurrency as well as distribution, and a lightweight actor model implementation that schedules all actors in a properly pre-dimensioned thread pool can outperform equivalent thread-based applications. However, the actor model did not enter the domain of native programming languages yet besides vendor-specific island solutions. With the open source library libcppa, we want to combine the ability to build reliable and distributed systems provided by the actor model with the performance and resource-efficiency of C++11.Comment: 10 page

A quantum genetic algorithm with quantum crossover and mutation operations

In the context of evolutionary quantum computing in the literal meaning, a quantum crossover operation has not been introduced so far. Here, we introduce a novel quantum genetic algorithm which has a quantum crossover procedure performing crossovers among all chromosomes in parallel for each generation. A complexity analysis shows that a quadratic speedup is achieved over its classical counterpart in the dominant factor of the run time to handle each generation.Comment: 21 pages, 1 table, v2: typos corrected, minor modifications in sections 3.5 and 4, v3: minor revision, title changed (original title: Semiclassical genetic algorithm with quantum crossover and mutation operations), v4: minor revision, v5: minor grammatical corrections, to appear in QI

Customisable Handling of Java References in Prolog Programs

Integration techniques for combining programs written in distinct language paradigms facilitate the implementation of specialised modules in the best language for their task. In the case of Java-Prolog integration, a known problem is the proper representation of references to Java objects on the Prolog side. To solve it adequately, multiple dimensions should be considered, including reference representation, opacity of the representation, identity preservation, reference life span, and scope of the inter-language conversion policies. This paper presents an approach that addresses all these dimensions, generalising and building on existing representation patterns of foreign references in Prolog, and taking inspiration from similar inter-language representation techniques found in other domains. Our approach maximises portability by making few assumptions about the Prolog engine interacting with Java (e.g., embedded or executed as an external process). We validate our work by extending JPC, an open-source integration library, with features supporting our approach. Our JPC library is currently compatible with three different open source Prolog engines (SWI, YAP} and XSB) by means of drivers. To appear in Theory and Practice of Logic Programming (TPLP).Comment: 10 pages, 2 figure