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, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.
Geany is a powerful, stable and lightweight programmer's text editor that provides tons of useful features without bogging down your workflow. It runs on Linux, Windows and MacOS is translated into over 40 languages, and has built-in support for more than 50 programming languages.
- Cross-platform PlatformIO IDE and Unified Debugger
- Static Code Analyzer and Remote Unit Testing
- Multi-platform and Multi-architecture Build System
- Firmware File Explorer and Memory Inspection
W. Lavrijsen, и A. Dutta. Proceedings of the 6th Workshop on Python for High-Performance and Scientific Computing, стр. 27--35. Piscataway, NJ, USA, IEEE Press, (2016)
D. Wu, L. Chen, Y. Zhou, и B. Xu. 2015 ACM/IEEE International Symposium on Empirical Software Engineering and Measurement (ESEM), стр. 1-10. (октября 2015)
V. Saraswat, R. Jagadeesan, M. Michael, и C. von Praun. PPoPP '07: Proceedings of the 12th ACM SIGPLAN symposium on Principles and practice of parallel programming, стр. 161--172. New York, NY, USA, ACM, (2007)