Package: ompBAM 1.16.0

(0) Installation and Quick-Start | Installation | Creating and testing an example ompBAM-based package | To create an ompBAM-based package from within RStudio: | (1) Requirements to setting up a new R package to include ompBAM | (1a) Making a new package that compiles with ompBAM | (1b) Dependencies required to compile with ompBAM | (1c) Make Files | (1d) OpenMP compatibility | (2) Step-by-step guide to creating your first ompBAM-powered package | (2a) Headers and Includes | (2b) Sanity check for number of threads | (2c) Opening BAM files with ompBAM | Note 3 things: | (2d) Obtaining chromosome names and lengths | (2e) Constructing a loop to read the BAM file using ompBAM | (2f) Processing BAM reads using an OpenMP parallel FOR loop | (2g) Getting thread-specific reads from ompBAM | (2g:i) Checking "validity" of reads and "realizing" reads | (2h) Counting chromosome-specific reads | (2h:i) Obtaining the chromosome ID of each aligned read | (2h:ii) Tallying reads to a variable external to the parallel FOR loop | (2i) Closing the BAM file | (2j) Summarizing the tallied reads | (2k) Adding a progress bar | (3) pbam_in function documentation | (3a) Constructor | Usage | Parameters | Details | Examples | (3b) openFile() | (3c) SetInputHandle() | (3d) closeFile() | (3e) obtainChrs() | Return value | (3f) fillReads() | (3g) supplyRead() | (3h) remainingThreadReadsBuffer(); | (3i) Progress and File Size Functions | (4) pbam1_t function documentation | (4a) Constructor | (4b) validate() | (4c) realize() | (4d) isReal() | (4e) Getters of Read Core Data | (4f) Getters of Cigar Data | (4g) Getters of Alignment Sequence and Quality score | (4h) Tag Getters | (5) SessionInfo