// File: /workspace/github_cpp_makefile_star2_O2/readmapping[P]alfalfa/src/options.cpp
// Function: mapOptions_t::printOptions()
void mapOptions_t::printOptions() {
    cerr << "ALFALFA was executed with following options: " << endl;
    cerr << "reference sequence\t\t" << ref_fasta << endl;
    if (!outputName.empty())
        cerr << "output file\t\t" << outputName << endl;
    if (!indexLocation.empty())
        cerr << "index location\t\t\t" << indexLocation << endl;
    if (!index_prefix.empty())
        cerr << "index prefix\t\t\t" << index_prefix << endl;
    cerr << "save index \t\t\t" << (saveIndex ? "yes" : "no") << endl;
    if (!unpairedQ.empty())
        cerr << "single-end reads\t\t\t" << unpairedQ << endl;
    if (!pair1.empty() && !pair2.empty()) {
        cerr << "mate 1   \t\t\t" << pair1 << endl;
        cerr << "mate 2   \t\t\t" << pair2 << endl;
    }
    cerr << "sparseness \t\t\t" << K << endl;
    cerr << "threads  \t\t\t" << query_threads << endl;
    cerr << "edit distance   \t\t\t" << alnOptions.errorPercent << endl;
    cerr << "min seed length\t\t\t" << alnOptions.minMemLength << endl;
    cerr << "auto seed length\t\t\t" << (alnOptions.fixedMinLength ? "no" : "yes") << endl;
    cerr << "max seed candidates\t\t\t" << alnOptions.maxSeedCandidates << endl;
    cerr << "max SMEM occurrence before mems are calculated " << alnOptions.maxSmemMemStart << endl;
    cerr << "min MEM length to consider for region selection " << alnOptions.minMemRegLength << endl;
    cerr << "max number of MEMs per SMEM for region selection " << alnOptions.maxRegionMems << endl;
    cerr << "type of seeds\t\t\t" << alnOptions.memType << endl;
    cerr << "rescue procedures on?\t\t\t" << (alnOptions.rescue ? "yes" : "no") << endl;
    cerr << "full dynamic programming for post-processing\t" << (alnOptions.fullDP ? "yes" : "no") << endl;
    cerr << "#alignments\t\t\t" << alnOptions.alignmentCount << endl;
    cerr << "#try and error\t\t\t" << alnOptions.maxTrial << endl;
    cerr << "min #alignments to decide mapq\t\t" << alnOptions.minTrial << endl;
    cerr << "min #alignments checks from best alignment?\t\t" << (alnOptions.maxTrialBest ? "yes" : "no") << endl;
    cerr << "always consider regions containing unique SMEMs\t\t" << (alnOptions.alwaysUnique ? "yes" : "no") << endl;
    cerr << "min query coverage\t\t" << alnOptions.minCoverage << endl;
    cerr << "use local alignment?\t\t\t" << (alnOptions.global ? "no" : "yes") << endl;
    if (!alnOptions.global) {
        cerr << "use band size\t\t\t" << alnOptions.fixedBandSize << endl;
    }
    cerr << "verbosity level\t\t\t" << alnOptions.print << endl;
    cerr << "debug info to file?" << (alnOptions.debugFile == NULL ? "no" : "yes") << endl;
    cerr << "calculate forward\t\t\t" << (alnOptions.noFW ? "no" : "yes") << endl;
    cerr << "calculate reverse\t\t\t" << (alnOptions.noRC ? "no" : "yes") << endl;
    cerr << "match score\t\t\t" << alnOptions.match << endl;
    cerr << "mismatch score\t\t\t" << alnOptions.mismatch << endl;
    cerr << "gap open score\t\t\t" << alnOptions.openGap << endl;
    cerr << "gap extend score\t\t\t" << alnOptions.extendGap << endl;
    if (!pair1.empty() && !pair2.empty()) {
        cerr << "paired options: " << endl;
        cerr << "paired mode\t\t\t" << pairedOpt.mode << endl;
        cerr << "type pairing\t\t\t" << pairedOpt.orientation << endl;
        cerr << "min insert size\t\t\t" << pairedOpt.minInsert << endl;
        cerr << "max insert size\t\t\t" << pairedOpt.maxInsert << endl;
        cerr << "allow overlap\t\t\t" << (pairedOpt.overlap ? "yes" : "no") << endl;
        cerr << "allow contained\t\t\t" << (pairedOpt.contain ? "yes" : "no") << endl;
        cerr << "allow discordant\t\t\t" << (pairedOpt.discordant ? "yes" : "no") << endl;
        cerr << "allow dovetail\t\t\t" << (pairedOpt.dovetail ? "yes" : "no") << endl;
        cerr << "allow mixed\t\t\t" << (pairedOpt.mixed ? "yes" : "no") << endl;
        cerr << "paired rescue?\t\t\t" << (pairedOpt.pairedRescue ? "yes" : "no") << endl;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x3eb2d(%rip), %r14     # 0x49fe8
leaq 0x2753a(%rip), %rsi     # 0x329fc
movq %r14, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x27551(%rip), %rsi     # 0x32a2a
movq %r14, %rdi
callq 0x72b0
leaq 0x70(%rbx), %rsi
movq %rax, %rdi
callq 0x7280
movq %rax, %rdi
callq 0x7160
cmpq $0x0, 0xe0(%rbx)
je 0xb52c
leaq 0xd8(%rbx), %r14
movq 0x3eadb(%rip), %rdi     # 0x49fe8
leaq 0x2752b(%rip), %rsi     # 0x32a3f
callq 0x72b0
movq %rax, %rdi
movq %r14, %rsi
callq 0x7280
movq %rax, %rdi
callq 0x7160
cmpq $0x0, 0xc0(%rbx)
je 0xb563
leaq 0xb8(%rbx), %r14
movq 0x3eaa4(%rip), %rdi     # 0x49fe8
leaq 0x27502(%rip), %rsi     # 0x32a4d
callq 0x72b0
movq %rax, %rdi
movq %r14, %rsi
callq 0x7280
movq %rax, %rdi
callq 0x7160
cmpq $0x0, 0x98(%rbx)
je 0xb59a
leaq 0x90(%rbx), %r14
movq 0x3ea6d(%rip), %rdi     # 0x49fe8
leaq 0x274dd(%rip), %rsi     # 0x32a5f
callq 0x72b0
movq %rax, %rdi
movq %r14, %rsi
callq 0x7280
movq %rax, %rdi
callq 0x7160
movq 0x3ea47(%rip), %rdi     # 0x49fe8
leaq 0x274c7(%rip), %rsi     # 0x32a6f
callq 0x72b0
leaq 0x26d1c(%rip), %rbp     # 0x322d0
cmpb $0x0, 0xb0(%rbx)
leaq 0x26d12(%rip), %r14     # 0x322d4
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
cmpq $0x0, 0x18(%rbx)
je 0xb60a
leaq 0x10(%rbx), %r15
movq 0x3e9fd(%rip), %rdi     # 0x49fe8
leaq 0x2748c(%rip), %rsi     # 0x32a7e
callq 0x72b0
movq %rax, %rdi
movq %r15, %rsi
callq 0x7280
movq %rax, %rdi
callq 0x7160
cmpq $0x0, 0x38(%rbx)
je 0xb66b
cmpq $0x0, 0x58(%rbx)
je 0xb66b
leaq 0x30(%rbx), %r15
leaq 0x50(%rbx), %r12
movq 0x3e9c1(%rip), %r13     # 0x49fe8
leaq 0x27464(%rip), %rsi     # 0x32a92
movq %r13, %rdi
callq 0x72b0
movq %rax, %rdi
movq %r15, %rsi
callq 0x7280
movq %rax, %rdi
callq 0x7160
leaq 0x2744f(%rip), %rsi     # 0x32a9f
movq %r13, %rdi
callq 0x72b0
movq %rax, %rdi
movq %r12, %rsi
callq 0x7280
movq %rax, %rdi
callq 0x7160
movq 0x3e976(%rip), %r15     # 0x49fe8
leaq 0x27433(%rip), %rsi     # 0x32aac
movq %r15, %rdi
callq 0x72b0
movl 0x4(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x27420(%rip), %rsi     # 0x32abb
movq %r15, %rdi
callq 0x72b0
movl 0x8(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x2740b(%rip), %rsi     # 0x32ac8
movq %r15, %rdi
callq 0x72b0
movsd 0x130(%rbx), %xmm0
movq %rax, %rdi
callq 0x7560
movq %rax, %rdi
callq 0x7160
leaq 0x273f8(%rip), %rsi     # 0x32adc
movq %r15, %rdi
callq 0x72b0
movl 0x138(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273e6(%rip), %rsi     # 0x32aef
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x13c(%rbx)
movq %rbp, %rsi
cmovneq %r14, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x273cd(%rip), %rsi     # 0x32b03
movq %r15, %rdi
callq 0x72b0
movl 0x140(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273bf(%rip), %rsi     # 0x32b1a
movq %r15, %rdi
callq 0x72b0
movl 0x144(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273ca(%rip), %rsi     # 0x32b4a
movq %r15, %rdi
callq 0x72b0
movl 0x148(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273d6(%rip), %rsi     # 0x32b7b
movq %r15, %rdi
callq 0x72b0
movl 0x14c(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273e3(%rip), %rsi     # 0x32bad
movq %r15, %rdi
callq 0x72b0
movl 0x188(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273cf(%rip), %rsi     # 0x32bbe
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x171(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x273bb(%rip), %rsi     # 0x32bd7
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x173(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x273bc(%rip), %rsi     # 0x32c05
movq %r15, %rdi
callq 0x72b0
movl 0x150(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x273a6(%rip), %rsi     # 0x32c14
movq %r15, %rdi
callq 0x72b0
movl 0x154(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x27393(%rip), %rsi     # 0x32c26
movq %r15, %rdi
callq 0x72b0
movl 0x158(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x2738f(%rip), %rsi     # 0x32c47
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x15c(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x27390(%rip), %rsi     # 0x32c75
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x170(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x27395(%rip), %rsi     # 0x32ca7
movq %r15, %rdi
callq 0x72b0
movsd 0x168(%rbx), %xmm0
movq %rax, %rdi
callq 0x7560
movq %rax, %rdi
callq 0x7160
leaq 0x27383(%rip), %rsi     # 0x32cbc
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x12a(%rbx)
movq %rbp, %rsi
cmovneq %r14, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
cmpb $0x0, 0x12a(%rbx)
jne 0xb991
movq 0x3e679(%rip), %rdi     # 0x49fe8
leaq 0x2735e(%rip), %rsi     # 0x32cd4
callq 0x72b0
movl 0x190(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
movq 0x3e650(%rip), %r15     # 0x49fe8
leaq 0x27346(%rip), %rsi     # 0x32ce5
movq %r15, %rdi
callq 0x72b0
movl 0x178(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x27334(%rip), %rsi     # 0x32cf8
movq %r15, %rdi
callq 0x72b0
cmpq $0x0, 0x180(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x2731a(%rip), %rsi     # 0x32d0c
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x174(%rbx)
movq %rbp, %rsi
cmovneq %r14, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x27302(%rip), %rsi     # 0x32d21
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x175(%rbx)
movq %rbp, %rsi
cmovneq %r14, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x272ed(%rip), %rsi     # 0x32d39
movq %r15, %rdi
callq 0x72b0
movl 0x100(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x272c5(%rip), %rsi     # 0x32d36
movq %r15, %rdi
callq 0x72b0
movl 0x104(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x272b2(%rip), %rsi     # 0x32d48
movq %r15, %rdi
callq 0x72b0
movl 0x108(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x2729f(%rip), %rsi     # 0x32d5a
movq %r15, %rdi
callq 0x72b0
movl 0x10c(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
cmpq $0x0, 0x38(%rbx)
je 0xbcbd
cmpq $0x0, 0x58(%rbx)
je 0xbcbd
movq 0x3e4f2(%rip), %r15     # 0x49fe8
leaq 0x27271(%rip), %rsi     # 0x32d6e
movq %r15, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x2726b(%rip), %rsi     # 0x32d7f
movq %r15, %rdi
callq 0x72b0
movl 0x1a8(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x27255(%rip), %rsi     # 0x32d8e
movq %r15, %rdi
callq 0x72b0
movl 0x1b0(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x27240(%rip), %rsi     # 0x32d9e
movq %r15, %rdi
callq 0x72b0
movl 0x198(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x2722e(%rip), %rsi     # 0x32db1
movq %r15, %rdi
callq 0x72b0
movl 0x19c(%rbx), %esi
movq %rax, %rdi
callq 0x75c0
movq %rax, %rdi
callq 0x7160
leaq 0x2721c(%rip), %rsi     # 0x32dc4
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x1a4(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x27200(%rip), %rsi     # 0x32dd5
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x1a3(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x271e6(%rip), %rsi     # 0x32de8
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x1a1(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x271cd(%rip), %rsi     # 0x32dfc
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x1a2(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x271b2(%rip), %rsi     # 0x32e0e
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x1a0(%rbx)
movq %r14, %rsi
cmovneq %rbp, %rsi
movq %rax, %rdi
callq 0x72b0
movq %rax, %rdi
callq 0x7160
leaq 0x27194(%rip), %rsi     # 0x32e1d
movq %r15, %rdi
callq 0x72b0
cmpb $0x0, 0x1ac(%rbx)
cmovneq %rbp, %r14
movq %rax, %rdi
movq %r14, %rsi
callq 0x72b0
movq %rax, %rdi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x7160
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq