GSTRUCT suite

A GsnapParam object stores parameters for gsnap. The function of the same name serves as its constructor.

GsnapParam(genome, unique_only = FALSE, molecule = c("RNA", "DNA"),
           max_mismatches = NULL,
           suboptimal_levels = 0L, mode = "standard",
           snps = NULL,
           npaths = if (unique_only) 1L else 100L,
           quiet_if_excessive = unique_only, nofails = unique_only,
           split_output = !unique_only,
           novelsplicing = FALSE, splicing = NULL, 
           nthreads = 1L, part = NULL, batch = "2",
           terminal_threshold = if (molecule == "DNA") 1000L else 2L,
           gmap_mode = if (molecule == "DNA") "none" else
                       "pairsearch,terminal,improve",
           clip_overlap = FALSE, ...)

`genome`	A GmapGenome object to align against
`unique_only`	Whether only alignments with a unique match should be output. The default is FALSE.
`molecule`	The type of molecule sequenced; used to determine appropriate parameter defaults.
`max_mismatches`	The maximum number of mismatches to allow per alignment. If NULL, then the value defaults to ((readlength + 2) / 12 - 2))
`suboptimal_levels`	Report suboptimal hits beyond best hit. The default is 0L.
`mode`	The alignment mode. It can be "standard", "cmet-stranded", "cmet-nonstranded", "atoi-stranded", or "atoi-nonstranded". The default is "standard".
`snps`	If not NULL, then a GmapSnps object. Provided SNPs will not count as mismatches.
`npaths`	The maximum number of paths to print.
`quiet_if_excessive`	If more than maximum number of paths are found, then no alignment from the read will be in the output.
`nofails`	Exclude failed alignments from output
`split_output`	Basename for multiple-file output, separately for nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results (up to 9 files, or 10 if –fails-as-input is selected, or 3 for single-end reads)
`novelsplicing`	Logical indicating whether to look for novel splicing events. FALSE is the default.
`splicing`	If not NULL, a GmapSplices object. NULL is the default.
`nthreads`	The number of worker threads gsnap should use to align.
`part`	If not NULL, then process only the i-th out of every n sequences e.g., 0/100 or 99/100 (useful for distributing jobs to a computer farm). If NULL, then all sequences are processed. NULL is the default.
`batch`	This argument allows control over gsnap's memory mapping and allocation. The default is mode 2. Mode 0: {offsets=allocate, positions=mmap, genome=mmap}, Mode 1: {offsets=allocate, positions=mmap & preload,genome=mmap}, Mode 2: {offsets=allocate, positions=mmap & preload,genome=mmap & preload}, Mode 3: {offsets=allocate, positions=allocate,genome=mmap & preload}, Mode 4: {offsets=allocate, positions=allocate,genome=allocate}
`...`	Additional parameters for gsnap. See gsnap's full documentation for those available.
`terminal_threshold`	If this number of mismatches is exceeded, GSNAP will attempt to align from one of the sequence, eventually giving up and discarding the rest of the sequence. This is called a “terminal alignment”. By setting this to a high value, we have effectively disabled it for DNA, since terminal alignments were motivated by splicing alignment problems and other special cases.
`gmap_mode`	Specifies the GMAP pipeline executed when GSNAP delegates to GMAP (a Smith-Waterman aligner) in difficult cases. We have disabled this for DNA, since such difficult cases are only anticipated in the context of splicing or complex rearrangements.
`clip_overlap`	Whether to equally clip paired ends that overlap each other (due to the fragment length being shorter than 2X the read length). This can be important for getting accurate counts from `bam_tally`.