// File: /workspace/github_c_makefile_star2_O1/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, 0x2f230(%rip)     # 0x42528
je 0x13a69
leaq 0x25de4(%rip), %rsi     # 0x390e9
leaq 0x2f1a4(%rip), %rdx     # 0x424b0
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movl 0x2ee84(%rip), %edx     # 0x421a0
movl 0x2ee82(%rip), %ecx     # 0x421a4
movl 0x2ee7f(%rip), %r8d     # 0x421a8
movl 0x2ee7c(%rip), %r9d     # 0x421ac
movsd 0x2ee88(%rip), %xmm0    # 0x421c0
movsd 0x2ee88(%rip), %xmm1    # 0x421c8
movsd 0x2ee88(%rip), %xmm2    # 0x421d0
movl 0x2ee62(%rip), %eax     # 0x421b0
movl %eax, (%rsp)
leaq 0x25dcc(%rip), %rsi     # 0x39124
movq %rbx, %rdi
movb $0x3, %al
callq 0x21c0
cmpl $0x0, 0x2ee47(%rip)     # 0x421b0
jle 0x133b9
leaq 0x26137(%rip), %r14     # 0x394a9
xorl %r15d, %r15d
movq 0x303b4(%rip), %rax     # 0x43730
movl 0x4(%rax,%r15,4), %edx
movq 0x303a0(%rip), %rax     # 0x43728
movl 0x4(%rax,%r15,4), %ecx
movq 0x303a4(%rip), %rax     # 0x43738
movl 0x4(%rax,%r15,4), %r8d
subl (%rax,%r15,4), %r8d
movq %rbx, %rdi
movq %r14, %rsi
xorl %eax, %eax
callq 0x21c0
movslq 0x2edff(%rip), %rax     # 0x421b0
incq %r15
cmpq %rax, %r15
jl 0x13375
movsd 0x2f017(%rip), %xmm0    # 0x423d8
leaq 0x25d8e(%rip), %rsi     # 0x39156
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2f006(%rip), %xmm0    # 0x423e0
leaq 0x25d7e(%rip), %rsi     # 0x3915f
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ef7d(%rip), %xmm0    # 0x42370
leaq 0x25d6e(%rip), %rsi     # 0x39168
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
cmpb $0x1, 0x2ede1(%rip)     # 0x421ec
jne 0x13460
movl 0x2eddd(%rip), %edx     # 0x421f0
leaq 0x25d57(%rip), %rsi     # 0x39171
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpl $0x0, 0x2edc5(%rip)     # 0x421f0
jle 0x13460
xorl %r15d, %r15d
leaq 0x24e93(%rip), %r14     # 0x382ca
movq 0x302ca(%rip), %rax     # 0x43708
movsd (%rax,%r15,8), %xmm0
movq %rbx, %rdi
movq %r14, %rsi
movb $0x1, %al
callq 0x21c0
incq %r15
movslq 0x2ed95(%rip), %rax     # 0x421f0
cmpq %rax, %r15
jl 0x13437
movl 0x2ed8e(%rip), %edx     # 0x421f4
leaq 0x25d0a(%rip), %rsi     # 0x39177
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movsd 0x2ed61(%rip), %xmm0    # 0x421e0
leaq 0x25cf7(%rip), %rsi     # 0x3917d
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ed40(%rip), %xmm0    # 0x421d8
leaq 0x25ce7(%rip), %rsi     # 0x39186
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x3015f(%rip), %xmm0    # 0x43610
leaq 0x25cd7(%rip), %rsi     # 0x3918f
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x3012e(%rip), %xmm0    # 0x435f8
leaq 0x25cc7(%rip), %rsi     # 0x39198
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movl 0x302c7(%rip), %edx     # 0x437a8
leaq 0x25cb9(%rip), %rsi     # 0x391a1
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movl 0x2eed8(%rip), %edx     # 0x423d0
leaq 0x25ca8(%rip), %rsi     # 0x391a7
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpl $0x0, 0x2eec0(%rip)     # 0x423d0
jle 0x13550
xorl %r15d, %r15d
leaq 0x25c91(%rip), %r14     # 0x391ad
movq 0x301cd(%rip), %rax     # 0x436f0
movl (%rax,%r15,4), %edx
movq 0x301ba(%rip), %rax     # 0x436e8
movsd (%rax,%r15,8), %xmm0
movq %rbx, %rdi
movq %r14, %rsi
movb $0x1, %al
callq 0x21c0
incq %r15
movslq 0x2ee85(%rip), %rax     # 0x423d0
cmpq %rax, %r15
jl 0x1351c
movl 0x2eca2(%rip), %edx     # 0x421f8
leaq 0x25c5a(%rip), %rsi     # 0x391b7
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
movsd 0x2ec91(%rip), %xmm0    # 0x42200
leaq 0x25c47(%rip), %rsi     # 0x391bd
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ec80(%rip), %xmm0    # 0x42208
leaq 0x25c37(%rip), %rsi     # 0x391c6
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ec6f(%rip), %xmm0    # 0x42210
movsd 0x2ec6f(%rip), %xmm1    # 0x42218
movsd 0x2ec6f(%rip), %xmm2    # 0x42220
movsd 0x2ec6f(%rip), %xmm3    # 0x42228
leaq 0x25c0f(%rip), %rsi     # 0x391cf
movq %rbx, %rdi
movb $0x4, %al
callq 0x21c0
movsd 0x2ec5e(%rip), %xmm0    # 0x42230
leaq 0x25c11(%rip), %rsi     # 0x391ea
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ed7d(%rip), %xmm0    # 0x42368
leaq 0x25c01(%rip), %rsi     # 0x391f3
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ec3c(%rip), %xmm0    # 0x42240
movsd 0x2ec3c(%rip), %xmm1    # 0x42248
movsd 0x2ec3c(%rip), %xmm2    # 0x42250
movsd 0x2ec3c(%rip), %xmm3    # 0x42258
movsd 0x2ec3c(%rip), %xmm4    # 0x42260
movsd 0x2ec3c(%rip), %xmm5    # 0x42268
movsd 0x2ec3c(%rip), %xmm6    # 0x42270
movsd 0x2ec3c(%rip), %xmm7    # 0x42278
movaps 0x2ec3c(%rip), %xmm8    # 0x42280
movaps 0x2ec44(%rip), %xmm9    # 0x42290
movaps 0x2ec4c(%rip), %xmm10   # 0x422a0
movaps 0x2ec54(%rip), %xmm11   # 0x422b0
movups %xmm11, 0x30(%rsp)
movups %xmm10, 0x20(%rsp)
movups %xmm9, 0x10(%rsp)
movups %xmm8, (%rsp)
leaq 0x25b82(%rip), %rsi     # 0x391fc
movq %rbx, %rdi
movb $0x8, %al
callq 0x21c0
movsd 0x2ed6c(%rip), %xmm0    # 0x423f8
leaq 0x25bcd(%rip), %rsi     # 0x39260
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ed73(%rip), %xmm0    # 0x42418
movsd 0x2ed73(%rip), %xmm1    # 0x42420
leaq 0x25bb5(%rip), %rsi     # 0x39269
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x2ed62(%rip), %xmm0    # 0x42428
movsd 0x2ed62(%rip), %xmm1    # 0x42430
leaq 0x25ba3(%rip), %rsi     # 0x39278
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x2ed91(%rip), %xmm0    # 0x42478
movsd 0x2ed91(%rip), %xmm1    # 0x42480
leaq 0x25b91(%rip), %rsi     # 0x39287
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x2ed48(%rip), %xmm0    # 0x42450
movsd 0x2ed48(%rip), %xmm1    # 0x42458
movl 0x2ed4a(%rip), %edx     # 0x42460
leaq 0x25b79(%rip), %rsi     # 0x39296
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x2ed59(%rip), %xmm0    # 0x42488
movsd 0x2ed59(%rip), %xmm1    # 0x42490
leaq 0x25b6a(%rip), %rsi     # 0x392a8
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x2ecf0(%rip), %xmm0    # 0x42440
movsd 0x2ecf0(%rip), %xmm1    # 0x42448
leaq 0x25b58(%rip), %rsi     # 0x392b7
movq %rbx, %rdi
movb $0x2, %al
callq 0x21c0
movsd 0x2ec77(%rip), %xmm0    # 0x423e8
leaq 0x25b4e(%rip), %rsi     # 0x392c6
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ebee(%rip), %xmm0    # 0x42378
leaq 0x25b3e(%rip), %rsi     # 0x392cf
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ecc5(%rip), %xmm0    # 0x42468
leaq 0x25b2e(%rip), %rsi     # 0x392d8
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2ec7c(%rip), %xmm0    # 0x42438
leaq 0x25b1e(%rip), %rsi     # 0x392e1
movq %rbx, %rdi
movb $0x1, %al
callq 0x21c0
movsd 0x2eafb(%rip), %xmm0    # 0x422d0
movsd 0x2eafb(%rip), %xmm1    # 0x422d8
movsd 0x2eafb(%rip), %xmm2    # 0x422e0
movsd 0x2eafb(%rip), %xmm3    # 0x422e8
movsd 0x2eafb(%rip), %xmm4    # 0x422f0
movsd 0x2eafb(%rip), %xmm5    # 0x422f8
movsd 0x2eafb(%rip), %xmm6    # 0x42300
movsd 0x2eafb(%rip), %xmm7    # 0x42308
movaps 0x2eafb(%rip), %xmm8    # 0x42310
movaps 0x2eb03(%rip), %xmm9    # 0x42320
movaps 0x2eb0b(%rip), %xmm10   # 0x42330
movaps 0x2eb13(%rip), %xmm11   # 0x42340
movups %xmm11, 0x30(%rsp)
movups %xmm10, 0x20(%rsp)
movups %xmm9, 0x10(%rsp)
movups %xmm8, (%rsp)
leaq 0x25a9f(%rip), %rsi     # 0x392ea
movq %rbx, %rdi
movb $0x8, %al
callq 0x21c0
cmpb $0x1, 0x2eb30(%rip)     # 0x4238c
jne 0x13874
leaq 0x25ae8(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x1, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2eb15(%rip)     # 0x42390
jne 0x13893
leaq 0x25ac9(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x2, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2eb02(%rip)     # 0x4239c
jne 0x138b2
leaq 0x25aaa(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x3, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2eadf(%rip)     # 0x42398
jne 0x138d1
leaq 0x25a8b(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x4, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ead0(%rip)     # 0x423a8
jne 0x138f0
leaq 0x25a6c(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x5, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2eaa9(%rip)     # 0x423a0
jne 0x1390f
leaq 0x25a4d(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x6, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ea8e(%rip)     # 0x423a4
jne 0x1392e
leaq 0x25a2e(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x7, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ea83(%rip)     # 0x423b8
jne 0x1394d
leaq 0x25a0f(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x8, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ea68(%rip)     # 0x423bc
jne 0x1396c
leaq 0x259f0(%rip), %rsi     # 0x3934d
movq %rbx, %rdi
movl $0x9, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ea21(%rip)     # 0x42394
jne 0x1398b
leaq 0x259d6(%rip), %rsi     # 0x39352
movq %rbx, %rdi
movl $0x59, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ea32(%rip)     # 0x423c4
jne 0x139aa
leaq 0x259b7(%rip), %rsi     # 0x39352
movq %rbx, %rdi
movl $0x76, %edx
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2ea17(%rip)     # 0x423c8
jne 0x139c9
leaq 0x25998(%rip), %rsi     # 0x39352
movq %rbx, %rdi
movl $0x78, %edx
xorl %eax, %eax
callq 0x21c0
leaq 0x25987(%rip), %rsi     # 0x39357
leaq 0x2eef9(%rip), %rdx     # 0x428d0
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2e99c(%rip)     # 0x42384
jne 0x13a02
leaq 0x2596c(%rip), %rsi     # 0x3935d
leaq 0x2f7d8(%rip), %rdx     # 0x431d0
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2e97f(%rip)     # 0x42388
jne 0x13a23
leaq 0x25951(%rip), %rsi     # 0x39363
leaq 0x2f837(%rip), %rdx     # 0x43250
movq %rbx, %rdi
xorl %eax, %eax
callq 0x21c0
cmpb $0x1, 0x2e986(%rip)     # 0x423b0
jne 0x13a42
leaq 0x2591f(%rip), %rsi     # 0x39352
movq %rbx, %rdi
movl $0x57, %edx
xorl %eax, %eax
callq 0x21c0
movl 0x2ea60(%rip), %edx     # 0x424a8
movq 0x2ec79(%rip), %rcx     # 0x426c8
leaq 0x25913(%rip), %rsi     # 0x39369
movq %rbx, %rdi
xorl %eax, %eax
addq $0x40, %rsp
popq %rbx
popq %r14
popq %r15
jmp 0x21c0
movq 0x2fc68(%rip), %rdx     # 0x436d8
leaq 0x2563e(%rip), %rsi     # 0x390b5
movq %rbx, %rdi
xorl %eax, %eax
addq $0x40, %rsp
popq %rbx
popq %r14
popq %r15
jmp 0x21c0