// File: readmapping[P]alfalfa/src/options.cpp
// Function: mapOptions_t::initOptions()
void mapOptions_t::initOptions() {
    K = 12;
    query_threads = 1;
    nucleotidesOnly = false;
    alnOptions.minMemLength = 40;
    alnOptions.fixedMinLength = false;
    alnOptions.memType = SMAM;
    alnOptions.sparseMult = 1;
    alnOptions.noFW = alnOptions.noRC = false;
    alnOptions.errorPercent = 0.08;
    alnOptions.print = 0;
    alnOptions.debugFile = NULL;
    alnOptions.match = 1; //(2,-1,-2,-1);
    alnOptions.mismatch = -4;
    alnOptions.openGap = -6;
    alnOptions.extendGap = -1;
    alnOptions.global = true;
    alnOptions.alignmentCount = 1;
    alnOptions.maxTrial = 10;
    alnOptions.minTrial = 5000;
    alnOptions.maxTrialBest = true;
    alnOptions.alwaysUnique = true;
    alnOptions.minCoverage = 0.25;
    alnOptions.rescue = true;
    alnOptions.noSparseQ = false;
    alnOptions.fullDP = false;
    alnOptions.maxSeedCandidates = 10000;
    alnOptions.maxSmemMemStart = 10;
    alnOptions.maxRegionMems = 20;
    alnOptions.minMemRegLength = 50; //SET TO AUTOMATIC VALUE
    alnOptions.scoresSetByUser = false;
    alnOptions.fixedBandSize = 100;
    pairedOpt.contain = true;
    pairedOpt.discordant = true;
    pairedOpt.dovetail = false;
    pairedOpt.maxInsert = 1000; //return to default!//
    pairedOpt.minInsert = 0; //return to default!//
    pairedOpt.mixed = true;
    pairedOpt.orientation = PAIR_FR;
    pairedOpt.overlap = true;
    pairedOpt.mode = 1;
    pairedOpt.pairedRescue = false;
    unpairedQ = pair1 = pair2 = ref_fasta = outputName = "";
    command = ALN;
    saveIndex = false;
    hasChild = true;
    hasSuflink = false;
    hasKmer = true;
    index_prefix = indexLocation = "";
}

// Assembly:
subq $0x18, %rsp
movq %rdi, 0x10(%rsp)
movq 0x10(%rsp), %rdi
movq %rdi, 0x8(%rsp)
movl $0xc, 0x4(%rdi)
movl $0x1, 0x8(%rdi)
movb $0x0, 0xf8(%rdi)
movl $0x28, 0x138(%rdi)
movb $0x0, 0x13c(%rdi)
movl $0x4, 0x188(%rdi)
movl $0x1, 0x18c(%rdi)
movb $0x0, 0x175(%rdi)
movb $0x0, 0x174(%rdi)
movsd 0x67205(%rip), %xmm0    # 0x798d8
movsd %xmm0, 0x130(%rdi)
movl $0x0, 0x178(%rdi)
movq $0x0, 0x180(%rdi)
movl $0x1, 0x100(%rdi)
movl $0xfffffffc, 0x104(%rdi) # imm = 0xFFFFFFFC
movl $0xfffffffa, 0x108(%rdi) # imm = 0xFFFFFFFA
movl $0xffffffff, 0x10c(%rdi) # imm = 0xFFFFFFFF
movb $0x1, 0x12a(%rdi)
movl $0x1, 0x150(%rdi)
movl $0xa, 0x154(%rdi)
movl $0x1388, 0x158(%rdi)    # imm = 0x1388
movb $0x1, 0x15c(%rdi)
movb $0x1, 0x170(%rdi)
movsd 0x6717d(%rip), %xmm0    # 0x798d0
movsd %xmm0, 0x168(%rdi)
movb $0x1, 0x171(%rdi)
movb $0x0, 0x172(%rdi)
movb $0x0, 0x173(%rdi)
movl $0x2710, 0x140(%rdi)    # imm = 0x2710
movl $0xa, 0x144(%rdi)
movl $0x14, 0x14c(%rdi)
movl $0x32, 0x148(%rdi)
movb $0x0, 0x129(%rdi)
movl $0x64, 0x190(%rdi)
movb $0x1, 0x1a3(%rdi)
movb $0x1, 0x1a1(%rdi)
movb $0x0, 0x1a2(%rdi)
movl $0x3e8, 0x19c(%rdi)     # imm = 0x3E8
movl $0x0, 0x198(%rdi)
movb $0x1, 0x1a0(%rdi)
movl $0x0, 0x1b0(%rdi)
movb $0x1, 0x1a4(%rdi)
movl $0x1, 0x1a8(%rdi)
movb $0x0, 0x1ac(%rdi)
addq $0xd8, %rdi
leaq 0x67255(%rip), %rsi     # 0x79a5e
callq 0x8570
movq 0x8(%rsp), %rdi
movq %rax, %rsi
addq $0x70, %rdi
callq 0x8060
movq 0x8(%rsp), %rdi
movq %rax, %rsi
addq $0x50, %rdi
callq 0x8060
movq 0x8(%rsp), %rdi
movq %rax, %rsi
addq $0x30, %rdi
callq 0x8060
movq 0x8(%rsp), %rdi
movq %rax, %rsi
addq $0x10, %rdi
callq 0x8060
movq 0x8(%rsp), %rdi
movl $0x2, (%rdi)
movb $0x0, 0xb0(%rdi)
movb $0x1, 0xb1(%rdi)
movb $0x0, 0xb2(%rdi)
movb $0x1, 0xb3(%rdi)
addq $0xb8, %rdi
leaq 0x671d7(%rip), %rsi     # 0x79a5e
callq 0x8570
movq 0x8(%rsp), %rdi
movq %rax, %rsi
addq $0x90, %rdi
callq 0x8060
addq $0x18, %rsp
retq
nopw %cs:(%rax,%rax)