test_gsnap_syscall_unique_only_TRUE <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            unique_only = TRUE,
                            gunzip=TRUE)
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   ##"unique_only=TRUE" means npath=1, no_fails is true, and
   ##split_output is false
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue(any(pieces == "--npaths=1"))
   checkTrue(any(pieces == "--nofails"))
   checkTrue(!any(pieces == "split-output"))
 }
 
 test_gsnap_syscall_unique_only_FALSE <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            unique_only = FALSE,
                            gunzip=TRUE)
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   ##"unique_only=FALSE" means npath=100L, no_fails is false, and
   ##split_output is true
   pieces <- unlist(strsplit(systemCall, " "))
   ##since npaths=100 is a default, "npaths" should not be in the
   ##command line
   checkTrue(!any(grepl("--npaths=", pieces)))
   checkTrue(!any(pieces == "--nofails"))
   checkTrue(sum(grepl("^--split-output=", pieces)) == 1)
 }
 
 test_gsnap_syscall_max_mismatches <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            unique_only = FALSE,
                            gunzip=TRUE,
                            max_mismatches=8)
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue(any(pieces == "--max-mismatches=8"))
 }
 
 test_gsnap_syscall_suboptimal_levels <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            unique_only = FALSE,
                            gunzip=TRUE,
                            suboptimal_levels=3)
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue(any(pieces == "--suboptimal-levels=3"))
 }
 
 test_gsnap_syscall_suboptimal_levels_default <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            unique_only = FALSE,
                            gunzip=TRUE,
                            suboptimal_levels=0)
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue(!any(grepl("^--suboptimal-levels=", pieces)))
 }
 
 test_gsnap_mode_incorrect <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            gunzip=TRUE,
                            mode="cmet")
   checkException(gsnap(input_a=fastqs["H1993.first"],
                        input_b=fastqs["H1993.last"],
                        params=gsnapParam))
 }
 
 test_gsnap_syscall_mode <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            gunzip=TRUE,
                            mode="cmet-stranded")
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue(any(pieces == "--mode=cmet-stranded"))
 }
 
 test_gsnap_syscall_novelsplicing_FALSE <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            novelsplicing = FALSE,
                            gunzip=TRUE)  
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue(sum(grepl("^--novelsplicing=", pieces)) == 0)
 }
 
 test_gsnap_syscall_novelsplicing_TRUE <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            unique_only = FALSE,
                            max_mismatches = NULL,
                            suboptimal_levels = 0, mode = "standard",
                            npaths = 10,
                            novelsplicing = TRUE,
                            splicing = NULL, 
                            nthreads = 1,
                            batch = 2L,
                            gunzip=TRUE)
   
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue("--novelsplicing=1" %in% pieces)
 }

 
 test_gsnap_syscall_nthreads_TRUE <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            nthreads=8,
                            gunzip=TRUE)
   
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue("--nthreads=8" %in% pieces)
 }
 
 test_gsnap_syscall_part <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            part="3/99",
                            gunzip=TRUE)
   
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue("--part=3/99" %in% pieces)
 }
 
 test_gsnap_syscall_batch <- function() {
   gmapGenome <- TP53Genome()
   fastqs <- LungCancerLines::LungCancerFastqFiles()
   gsnapParam <- GsnapParam(genome = gmapGenome,
                            batch=4,
                            gunzip=TRUE)  
   systemCall <- gmapR:::asSystemCall(gsnap(input_a=fastqs["H1993.first"],
                                            input_b=fastqs["H1993.last"],
                                            params=gsnapParam))
   pieces <- unlist(strsplit(systemCall, " "))
   checkTrue("--batch=4" %in% pieces)
 }