// File: /workspace/github_c_makefile_star2_O2/dapogon[P]cellcoal/src/cellcoal.c
// Function: PrintCommandLine
static void PrintCommandLine (FILE *fp, int argc,char **argv)
    {
	int i;

	if (readingParameterFile == NO)
		fprintf (fp, "Command line arguments (some might not affect) = %s", CommandLine);
	else
		{
		fprintf (fp, "Parameter file [\"%s\"] arguments (some might not affect) = ", parameterFile);

		/* Coalescent */
		fprintf (fp, " -n%d -s%d -l%d -e%d -g%2.1e -K%2.1e -L%2.1e -h%d", numDataSets, numCells, numSites, N, growthRate, birthRate, deathRate, numPeriods);
		for (i=1; i<=numPeriods; i++)
			fprintf (fp, " %d %d %d", Nbegin[i], Nend[i], cumDuration[i]-cumDuration[i-1]);

		/* Post-coalescent */
		fprintf (fp, " -k%2.1e", transformingBranchLengthRatio);
		fprintf (fp, " -q%2.1e", healthyTipBranchLengthRatio);
		fprintf (fp, " -i%6.4f", alphaBranches);
		if (doTreeRateSwitches == YES)
			{
			fprintf (fp, " -N%d", numTreeRateSwitches);
			for (i=0; i<numTreeRateSwitches; i++)
				fprintf (fp, " %4.2f", treeRateSwitchMultiplier[i]);
			}
		
		/* Mutation model */
		fprintf (fp, " -b%d", alphabet);
		fprintf (fp, " -c%2.1e", SNPrate);
		fprintf (fp, " -u%2.1e", mutationRate);
		fprintf (fp, " -d%2.1e", deletionRate);
		fprintf (fp, " -H%2.1e", CNLOHrate);
		fprintf (fp, " -j%d", numFixedMutations);
		fprintf (fp, " -S%d", numUserSignatures);
		for (i=0; i<numUserSignatures; i++)
			fprintf (fp, " %d %4.2f", signatureID[i], signatureWeight[i]);
		fprintf (fp, " -m%d", altModel);
		fprintf (fp, " -p%6.4f", propAltModelSites);
		fprintf (fp, " -w%6.4f", nonISMRelMutRate);
		fprintf (fp, " -f%3.2f %3.2f %3.2f %3.2f", freq[0], freq[1], freq[2], freq[3]);
		fprintf (fp, " -t%6.4f", titv);
		fprintf (fp, " -a%6.4f", alphaSites);
		fprintf (fp, " -r%3.2f %3.2f %3.2f %3.2f  %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f", Mij[0][0], Mij[0][1], Mij[0][2], Mij[0][3]
		, Mij[1][0], Mij[1][1], Mij[1][2], Mij[1][3],  Mij[2][0], Mij[2][1], Mij[2][2], Mij[2][3],  Mij[3][0], Mij[3][1], Mij[3][2], Mij[3][3]);

		/* scWGA */
		fprintf (fp, " -D%2.1e", fixedADOrate);
		fprintf (fp, " -P%2.1e %2.1e", meanADOcell, varADOcell);
		fprintf (fp, " -Q%2.1e %2.1e", meanADOsite, varADOsite);
		fprintf (fp, " -I%2.1e %2.1e", meanAllelicImbalance, varAllelicImbalance);
		fprintf (fp, " -A%2.1e %2.1e %d", meanAmplificationError, varAmplificationError, simulateOnlyTwoTemplates);
		fprintf (fp, " -B%2.1e %2.1e", meanDoubletRate, varDoubletRate);

		/* GENOTYPING */
		fprintf (fp, " -G%2.1e %2.1e", meanGenotypingError, varGenotypingError);

		/* NGS */
		fprintf (fp, " -C%3.2f", coverage);
		fprintf (fp, " -V%6.4f", alphaCoverage);
		fprintf (fp, " -R%2.1e", haploidCoverageReduction);
		fprintf (fp, " -E%2.1e", sequencingError);
		fprintf (fp, " -X%3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f %3.2f", Eij[0][0], Eij[0][1], Eij[0][2], Eij[0][3]
		, Eij[1][0], Eij[1][1], Eij[1][2], Eij[1][3],  Eij[2][0], Eij[2][1], Eij[2][2], Eij[2][3],  Eij[3][0], Eij[3][1], Eij[3][2], Eij[3][3]);

		/* Output */
		if (doPrintSNVgenotypes == YES)
			fprintf (fp, " -%d", 1);
		if (doPrintSNVhaplotypes == YES)
			fprintf (fp, " -%d", 2);
		if (doPrintFullGenotypes == YES)
			fprintf (fp, " -%d", 3);
		if (doPrintFullHaplotypes == YES)
			fprintf (fp, " -%d", 4);
		if (doPrintAncestors == YES)
			fprintf (fp, " -%d", 5);
		if (doPrintTree == YES)
			fprintf (fp, " -%d", 6);
		if (doPrintTimes == YES)
			fprintf (fp, " -%d", 7);
		if (doPrintCATG == YES)
			fprintf (fp, " -%d", 8);
		if (doPrintPILEUP == YES)
			fprintf (fp, " -%d", 9);
		if (doPrintTrueHaplotypes == YES)
			fprintf (fp, " -%c", 'Y');
		if (doPrintSeparateReplicates == YES)
			fprintf (fp, " -%c", 'v');
		if (doPrintIUPAChaplotypes == YES)
			fprintf (fp, " -%c", 'x');
		fprintf (fp, " -o%s", resultsDir);
		if (doUserTree == YES)
			fprintf (fp, " -T%s", userTreeFile);
		if (doUserGenome == YES)
			fprintf (fp, " -U%s", userGenomeFile);

		/* Other */
		if (doTumorNames == YES)
			fprintf (fp, " -%c", 'W');
		fprintf (fp, " -y%d -#%ld", noisy, originalSeed);
		}
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x40, %rsp
movq %rdi, %rbx
cmpb $0x0, 0x2025d(%rip)     # 0x30528
je 0x10a0c
leaq 0x13e3b(%rip), %rsi     # 0x24113
leaq 0x201d1(%rip), %rdx     # 0x304b0
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movl 0x1feb1(%rip), %edx     # 0x301a0
movl 0x1feaf(%rip), %ecx     # 0x301a4
movl 0x1feac(%rip), %r8d     # 0x301a8
movl 0x1fea9(%rip), %r9d     # 0x301ac
movsd 0x1feb5(%rip), %xmm0    # 0x301c0
movsd 0x1feb5(%rip), %xmm1    # 0x301c8
movsd 0x1feb5(%rip), %xmm2    # 0x301d0
movl 0x1fe8f(%rip), %eax     # 0x301b0
movl %eax, (%rsp)
leaq 0x13e23(%rip), %rsi     # 0x2414e
movq %rbx, %rdi
movb $0x3, %al
callq 0x21c0
pushq $0x1
popq %r15
leaq 0x14193(%rip), %r14     # 0x244d3
movslq 0x1fe69(%rip), %rax     # 0x301b0
cmpq %rax, %r15
jg 0x10384
movq 0x213dd(%rip), %rax     # 0x31730
movl (%rax,%r15,4), %edx
movq 0x213ca(%rip), %rax     # 0x31728
movl (%rax,%r15,4), %ecx
movq 0x213cf(%rip), %rax     # 0x31738
movl (%rax,%r15,4), %r8d
subl -0x4(%rax,%r15,4), %r8d
movq %rbx, %rdi
movq %r14, %rsi
xorl %eax, %eax
callq 0x21c0
incq %r15
jmp 0x10340
movsd 0x2004c(%rip), %xmm0    # 0x303d8
leaq 0x13ded(%rip), %rsi     # 0x24180
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2003b(%rip), %xmm0    # 0x303e0
leaq 0x13ddd(%rip), %rsi     # 0x24189
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1ffb2(%rip), %xmm0    # 0x30370
leaq 0x13dcd(%rip), %rsi     # 0x24192
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
cmpb $0x1, 0x1fe16(%rip)     # 0x301ec
jne 0x10424
movl 0x1fe12(%rip), %edx     # 0x301f0
leaq 0x13db6(%rip), %rsi     # 0x2419b
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
leaq 0x12efb(%rip), %r14     # 0x232f4
movslq 0x1fdf0(%rip), %rax     # 0x301f0
cmpq %rax, %r15
jge 0x10424
movq 0x212fc(%rip), %rax     # 0x31708
movsd (%rax,%r15,8), %xmm0
movq %rbx, %rdi
movq %r14, %rsi
movb $0x1, %al
callq 0x21c0
incq %r15
jmp 0x103f9
movl 0x1fdca(%rip), %edx     # 0x301f4
leaq 0x13d70(%rip), %rsi     # 0x241a1
xorl %r15d, %r15d
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movsd 0x1fd9a(%rip), %xmm0    # 0x301e0
leaq 0x13d5a(%rip), %rsi     # 0x241a7
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fd79(%rip), %xmm0    # 0x301d8
leaq 0x13d4a(%rip), %rsi     # 0x241b0
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x21198(%rip), %xmm0    # 0x31610
leaq 0x13d3a(%rip), %rsi     # 0x241b9
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x21167(%rip), %xmm0    # 0x315f8
leaq 0x13d2a(%rip), %rsi     # 0x241c2
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movl 0x21300(%rip), %edx     # 0x317a8
leaq 0x13d1c(%rip), %rsi     # 0x241cb
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movl 0x1ff11(%rip), %edx     # 0x303d0
leaq 0x13d0b(%rip), %rsi     # 0x241d1
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
leaq 0x13d00(%rip), %r14     # 0x241d7
movslq 0x1fef2(%rip), %rax     # 0x303d0
cmpq %rax, %r15
jge 0x1050d
movq 0x21206(%rip), %rax     # 0x316f0
movl (%rax,%r15,4), %edx
movq 0x211f3(%rip), %rax     # 0x316e8
movsd (%rax,%r15,8), %xmm0
movq %rbx, %rdi
movq %r14, %rsi
movb $0x1, %al
callq 0x21c0
incq %r15
jmp 0x104d7
movl 0x1fce5(%rip), %edx     # 0x301f8
leaq 0x13cc7(%rip), %rsi     # 0x241e1
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movsd 0x1fcd4(%rip), %xmm0    # 0x30200
leaq 0x13cb4(%rip), %rsi     # 0x241e7
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fcc3(%rip), %xmm0    # 0x30208
leaq 0x13ca4(%rip), %rsi     # 0x241f0
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fcb2(%rip), %xmm0    # 0x30210
movsd 0x1fcb2(%rip), %xmm1    # 0x30218
movsd 0x1fcb2(%rip), %xmm2    # 0x30220
movsd 0x1fcb2(%rip), %xmm3    # 0x30228
leaq 0x13c7c(%rip), %rsi     # 0x241f9
movq %rbx, %rdi
movb $0x4, %al
callq 0x21c0
movsd 0x1fca1(%rip), %xmm0    # 0x30230
leaq 0x13c7e(%rip), %rsi     # 0x24214
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fdc0(%rip), %xmm0    # 0x30368
leaq 0x13c6e(%rip), %rsi     # 0x2421d
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fc7f(%rip), %xmm0    # 0x30240
movsd 0x1fc7f(%rip), %xmm1    # 0x30248
movsd 0x1fc7f(%rip), %xmm2    # 0x30250
movsd 0x1fc7f(%rip), %xmm3    # 0x30258
movsd 0x1fc7f(%rip), %xmm4    # 0x30260
movsd 0x1fc7f(%rip), %xmm5    # 0x30268
movsd 0x1fc7f(%rip), %xmm6    # 0x30270
movsd 0x1fc7f(%rip), %xmm7    # 0x30278
movaps 0x1fc7f(%rip), %xmm8    # 0x30280
movaps 0x1fc87(%rip), %xmm9    # 0x30290
movaps 0x1fc8f(%rip), %xmm10   # 0x302a0
movaps 0x1fc97(%rip), %xmm11   # 0x302b0
movups %xmm11, 0x30(%rsp)
movups %xmm10, 0x20(%rsp)
movups %xmm9, 0x10(%rsp)
movups %xmm8, (%rsp)
leaq 0x13bef(%rip), %rsi     # 0x24226
movq %rbx, %rdi
movb $0x8, %al
callq 0x21c0
movsd 0x1fdaf(%rip), %xmm0    # 0x303f8
leaq 0x13c3a(%rip), %rsi     # 0x2428a
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fdb6(%rip), %xmm0    # 0x30418
movsd 0x1fdb6(%rip), %xmm1    # 0x30420
leaq 0x13c22(%rip), %rsi     # 0x24293
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x1fda5(%rip), %xmm0    # 0x30428
movsd 0x1fda5(%rip), %xmm1    # 0x30430
leaq 0x13c10(%rip), %rsi     # 0x242a2
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x1fdd4(%rip), %xmm0    # 0x30478
movsd 0x1fdd4(%rip), %xmm1    # 0x30480
leaq 0x13bfe(%rip), %rsi     # 0x242b1
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x1fd8b(%rip), %xmm0    # 0x30450
movsd 0x1fd8b(%rip), %xmm1    # 0x30458
movl 0x1fd8d(%rip), %edx     # 0x30460
leaq 0x13be6(%rip), %rsi     # 0x242c0
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x1fd9c(%rip), %xmm0    # 0x30488
movsd 0x1fd9c(%rip), %xmm1    # 0x30490
leaq 0x13bd7(%rip), %rsi     # 0x242d2
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x1fd33(%rip), %xmm0    # 0x30440
movsd 0x1fd33(%rip), %xmm1    # 0x30448
leaq 0x13bc5(%rip), %rsi     # 0x242e1
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x1fcba(%rip), %xmm0    # 0x303e8
leaq 0x13bbb(%rip), %rsi     # 0x242f0
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fc31(%rip), %xmm0    # 0x30378
leaq 0x13bab(%rip), %rsi     # 0x242f9
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fd08(%rip), %xmm0    # 0x30468
leaq 0x13b9b(%rip), %rsi     # 0x24302
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fcbf(%rip), %xmm0    # 0x30438
leaq 0x13b8b(%rip), %rsi     # 0x2430b
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x1fb3e(%rip), %xmm0    # 0x302d0
movsd 0x1fb3e(%rip), %xmm1    # 0x302d8
movsd 0x1fb3e(%rip), %xmm2    # 0x302e0
movsd 0x1fb3e(%rip), %xmm3    # 0x302e8
movsd 0x1fb3e(%rip), %xmm4    # 0x302f0
movsd 0x1fb3e(%rip), %xmm5    # 0x302f8
movsd 0x1fb3e(%rip), %xmm6    # 0x30300
movsd 0x1fb3e(%rip), %xmm7    # 0x30308
movaps 0x1fb3e(%rip), %xmm8    # 0x30310
movaps 0x1fb46(%rip), %xmm9    # 0x30320
movaps 0x1fb4e(%rip), %xmm10   # 0x30330
movaps 0x1fb56(%rip), %xmm11   # 0x30340
movups %xmm11, 0x30(%rsp)
movups %xmm10, 0x20(%rsp)
movups %xmm9, 0x10(%rsp)
movups %xmm8, (%rsp)
leaq 0x13b0c(%rip), %rsi     # 0x24314
movq %rbx, %rdi
movb $0x8, %al
callq 0x21c0
cmpb $0x1, 0x1fb73(%rip)     # 0x3038c
jne 0x1082f
leaq 0x13b55(%rip), %rsi     # 0x24377
pushq $0x1
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fb5a(%rip)     # 0x30390
jne 0x1084c
leaq 0x13b38(%rip), %rsi     # 0x24377
pushq $0x2
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fb49(%rip)     # 0x3039c
jne 0x10869
leaq 0x13b1b(%rip), %rsi     # 0x24377
pushq $0x3
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fb28(%rip)     # 0x30398
jne 0x10886
leaq 0x13afe(%rip), %rsi     # 0x24377
pushq $0x4
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fb1b(%rip)     # 0x303a8
jne 0x108a3
leaq 0x13ae1(%rip), %rsi     # 0x24377
pushq $0x5
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1faf6(%rip)     # 0x303a0
jne 0x108c0
leaq 0x13ac4(%rip), %rsi     # 0x24377
pushq $0x6
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fadd(%rip)     # 0x303a4
jne 0x108dd
leaq 0x13aa7(%rip), %rsi     # 0x24377
pushq $0x7
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fad4(%rip)     # 0x303b8
jne 0x108fa
leaq 0x13a8a(%rip), %rsi     # 0x24377
pushq $0x8
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fabb(%rip)     # 0x303bc
jne 0x10917
leaq 0x13a6d(%rip), %rsi     # 0x24377
pushq $0x9
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fa76(%rip)     # 0x30394
jne 0x10934
leaq 0x13a55(%rip), %rsi     # 0x2437c
pushq $0x59
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fa89(%rip)     # 0x303c4
jne 0x10951
leaq 0x13a38(%rip), %rsi     # 0x2437c
pushq $0x76
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1fa70(%rip)     # 0x303c8
jne 0x1096e
leaq 0x13a1b(%rip), %rsi     # 0x2437c
pushq $0x78
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
leaq 0x13a0c(%rip), %rsi     # 0x24381
leaq 0x1ff54(%rip), %rdx     # 0x308d0
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1f9f7(%rip)     # 0x30384
jne 0x109a7
leaq 0x139f1(%rip), %rsi     # 0x24387
leaq 0x20833(%rip), %rdx     # 0x311d0
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1f9da(%rip)     # 0x30388
jne 0x109c8
leaq 0x139d6(%rip), %rsi     # 0x2438d
leaq 0x20892(%rip), %rdx     # 0x31250
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x1f9e1(%rip)     # 0x303b0
jne 0x109e5
leaq 0x139a4(%rip), %rsi     # 0x2437c
pushq $0x57
popq %rdx
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movl 0x1fabd(%rip), %edx     # 0x304a8
movq 0x1fcd6(%rip), %rcx     # 0x306c8
leaq 0x1399a(%rip), %rsi     # 0x24393
movq %rbx, %rdi
xorl %eax, %eax
addq $0x40, %rsp
popq %rbx
popq %r14
popq %r15
jmp 0x21c0
movq 0x20cc5(%rip), %rdx     # 0x316d8
leaq 0x136c5(%rip), %rsi     # 0x240df
movq %rbx, %rdi
xorl %eax, %eax
addq $0x40, %rsp
popq %rbx
popq %r14
popq %r15
jmp 0x21c0