Retrieve start positions of aligned read sequences from BioMap object
Start = getStart(BioObj)
Start = getStart(BioObj, Subset)
Start = getStart(BioObj) returns Start, a vector of integers specifying the start position of aligned read sequences with respect to the position numbers in the reference sequence from a BioMap object.
Start = getStart(BioObj, Subset) returns a start position for only read sequences specified by Subset.
Object of the BioMap class.
One of the following to specify a subset of the elements in BioObj:
Start property of a subset of elements in BioObj. It is a vector of integers specifying the start position of aligned read sequences with respect to the position numbers in the reference sequence. It includes the start positions for only read sequences specified by Subset.
Construct a BioMap object, and then retrieve the start position for different sequences in the object:
% Construct a BioMap object from a SAM file BMObj1 = BioMap('ex1.sam'); % Retrieve the start property of the second element in the object Start_2 = getStart(BMObj1, 2)
Start_2 = 3
% Retrieve the start properties of the first and third elements in % the object Start_1_3 = getStart(BMObj1, [1 3])
Start_1_3 = 1 5
% Retrieve the start properties of all elements in the object Start_All = getStart(BMObj1);
An alternative to using the getStart method is to use dot indexing with the Start property:
In the previous syntax, Indices is a vector of positive integers or a logical vector. Indices cannot be a cell array of strings containing sequence headers.