Methods and apparatus for sorting data
First Claim
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1. A method for data processing, comprising:
- (a) obtaining a particular string data value from among a plurality of string data values, wherein each of the plurality of string data values comprises a portion of a genome sequence, and wherein the plurality of string data values is obtained from a genome sequence machine;
(b) mapping with a programmed computer processor the particular string data value to a particular data container among a plurality of data containers, wherein each of the plurality of string data values is addressable by a position in the genome sequence such that the plurality of data containers is ordered with respect to the genome sequence;
(c) appending a data item comprising the particular string data value to the particular data container in a computer memory;
(d) repeating (b)-(c) with the programmed computer processor for all of the plurality of string data values; and
(e) outputting a continuous output sequence generated from (a)-(d), wherein (a)-(d) are performed in the absence of sorting the plurality of string data values.
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Abstract
A computer implemented system for genomic data sorting, comprising alignment and position mapping. The system maps each read to a position on the reference genome with which the read is associated, followed by sorting these reads by their mapped positions.
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Citations
7 Claims
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1. A method for data processing, comprising:
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(a) obtaining a particular string data value from among a plurality of string data values, wherein each of the plurality of string data values comprises a portion of a genome sequence, and wherein the plurality of string data values is obtained from a genome sequence machine; (b) mapping with a programmed computer processor the particular string data value to a particular data container among a plurality of data containers, wherein each of the plurality of string data values is addressable by a position in the genome sequence such that the plurality of data containers is ordered with respect to the genome sequence; (c) appending a data item comprising the particular string data value to the particular data container in a computer memory; (d) repeating (b)-(c) with the programmed computer processor for all of the plurality of string data values; and (e) outputting a continuous output sequence generated from (a)-(d), wherein (a)-(d) are performed in the absence of sorting the plurality of string data values. - View Dependent Claims (2, 3, 4, 5, 6, 7)
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Specification