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sort samtools sort -o sorted_out unsorted_in.bam. Read the specified unsorted_in.bam as input, sort it by aligned read position, and write it out to sorted_out. Type of output can be either sam, bam, or cram, and will be determined automatically by sorted_out's file-extension. samtools sort -m 5000000 unsorted_in.bam sorted_out
The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is present.
The Z-ordering can be used to efficiently build a quadtree (2D) or octree (3D) for a set of points. [5] [6] The basic idea is to sort the input set according to Z-order.Once sorted, the points can either be stored in a binary search tree and used directly, which is called a linear quadtree, [7] or they can be used to build a pointer based quadtree.
sort is a generic function in the C++ Standard Library for doing comparison sorting.The function originated in the Standard Template Library (STL).. The specific sorting algorithm is not mandated by the language standard and may vary across implementations, but the worst-case asymptotic complexity of the function is specified: a call to sort must perform no more than O(N log N) comparisons ...
Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute , and became widely known through its implementation within the SAMtools ...
A database index is a data structure that improves the speed of data retrieval operations on a database table at the cost of additional writes and storage space to maintain the index data structure. Indexes are used to quickly locate data without having to search every row in a database table every time said table is accessed.
The top-k data structure at each node is constructed based on the values existing in the subtrees of that node and is meant to answer one-sided range top-k queries. Please note that for a one-dimensional array A {\displaystyle A} , a range tree can be constructed by dividing A {\displaystyle A} into two halves and recursing on both halves ...
In computer science, integer sorting is the algorithmic problem of sorting a collection of data values by integer keys. Algorithms designed for integer sorting may also often be applied to sorting problems in which the keys are floating point numbers, rational numbers, or text strings. [1]