// File: /workspace/github_c_makefile_star2_O0/ToniWestbrook[P]paladin/align.c
// Function: renderAlignUsage
int renderAlignUsage(const mem_opt_t * passOptions) {
	fprintf(stderr, "\n");
	fprintf(stderr, "Usage: paladin align [options] <idxbase> <in.fq>\n\n");

	fprintf(stderr, "Gene detection options:\n\n");
    fprintf(stderr, "       -q            disable ORF detection and treat input as transcript sequence\n");
    fprintf(stderr, "       -p            disable ORF detection and treat input as protein sequence\n");
	fprintf(stderr, "       -b            disable brute force detection\n");
	fprintf(stderr, "       -J            do not adjust minimum ORF length (constant value) for shorter read lengths\n");
	fprintf(stderr, "       -f INT        minimum ORF length accepted (as constant value) [%d]\n", passOptions->min_orf_len);
	fprintf(stderr, "       -F FLOAT      minimum ORF length accepted (as percentage of read length) [%.2f]\n", passOptions->min_orf_percent);
    fprintf(stderr, "       -z INT[,...]  Genetic code used for translation (-z ? for full list) [1]\n");    

	fprintf(stderr, "\nAlignment options:\n\n");
	fprintf(stderr, "       -t INT        number of threads [%d]\n", passOptions->n_threads);
	fprintf(stderr, "       -k INT        minimum seed length [%d]\n", passOptions->min_seed_len);
	fprintf(stderr, "       -d INT        off-diagonal X-dropoff [%d]\n", passOptions->zdrop);
	fprintf(stderr, "       -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", passOptions->split_factor);
	fprintf(stderr, "       -y INT        seed occurrence for the 3rd round seeding [%ld]\n", (long)passOptions->max_mem_intv);
    //fprintf(stderr, "       -s INT        look for internal seeds inside a seed with less than INT occ [%d]\n", passOptions->split_width); // Disabled in BWA
	fprintf(stderr, "       -c INT        skip seeds with more than INT occurrences [%d]\n", passOptions->max_occ);
	fprintf(stderr, "       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", passOptions->drop_ratio);
	fprintf(stderr, "       -W INT        discard a chain if seeded bases shorter than INT [0]\n");
	fprintf(stderr, "       -m INT        perform at most INT rounds of mate rescues for each read [%d]\n", passOptions->max_matesw);
	//fprintf(stderr, "       -S            skip mate rescue\n");
	//fprintf(stderr, "       -P            skip pairing; mate rescue performed unless -S also in use\n");
	fprintf(stderr, "       -e            discard full-length exact matches\n");

	fprintf(stderr, "\nScoring options:\n\n");
	fprintf(stderr, "       -A INT        score for a sequence match, which scales options -TdBOELU unless overridden [%d]\n", passOptions->a);
	fprintf(stderr, "       -B INT        penalty for a mismatch [%d]\n", passOptions->b);
	fprintf(stderr, "       -O INT[,INT]  gap open penalties for deletions and insertions [%d,%d]\n", passOptions->o_del, passOptions->o_ins);
	fprintf(stderr, "       -E INT[,INT]  gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [%d,%d]\n", passOptions->e_del, passOptions->e_ins);
	fprintf(stderr, "       -L INT[,INT]  penalty for 5'- and 3'-end clipping [%d,%d]\n", passOptions->pen_clip5, passOptions->pen_clip3);
	fprintf(stderr, "       -U INT        penalty for an unpaired read pair [%d]\n\n", passOptions->pen_unpaired);
	fprintf(stderr, "       -x STR        read type. Setting -x changes multiple parameters unless overriden [null]\n");
	fprintf(stderr, "                     pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  (PacBio reads to ref)\n");
	fprintf(stderr, "                     ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0  (Oxford Nanopore 2D-reads to ref)\n");
	fprintf(stderr, "                     intractg: -B9 -O16 -L5  (intra-species contigs to ref)\n");
//		fprintf(stderr, "                     pbread: -k13 -W40 -c1000 -r10 -A1 -B1 -O1 -E1 -N25 -FeaD.001\n");
	fprintf(stderr, "\nInput/output options:\n\n");
	fprintf(stderr, "       -o STR        activate PALADIN reporting using STR as an output file prefix.  Files generated as follows:\n");
	fprintf(stderr, "                        STR.sam - alignment data (will not be sent to stdout)\n");
	fprintf(stderr, "                        STR_uniprot.tsv - Tab delimited UniProt report (normal alignment mode)\n");
	fprintf(stderr, "                        STR_uniprot_primary.tsv - Tab delimited UniProt report, primary alignments (all alignments mode)\n");
	fprintf(stderr, "                        STR_uniprot_secondary.tsv - Tab delimited UniProt report, secondary alignments (all alignments mode)\n\n");
	fprintf(stderr, "       -u INT        report type generated when using reporting and a UniProt reference [%d]\n", passOptions->outputType);
	fprintf(stderr, "                        0: Simple ID summary report\n");
	fprintf(stderr, "                        1: Detailed report (Contacts uniprot.org)\n\n");
    fprintf(stderr, "       -P STR        HTTP or SOCKS proxy address\n");
	fprintf(stderr, "       -g            generate detected ORF nucleotide sequence FASTA\n");
	fprintf(stderr, "       -n            keep protein sequence after alignment\n");
	//fprintf(stderr, "       -p            smart pairing (ignoring in2.fq)\n");
	fprintf(stderr, "       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n");
	fprintf(stderr, "       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n");
	fprintf(stderr, "       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
	fprintf(stderr, "\n");
	fprintf(stderr, "       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [%d]\n", bwa_verbose);
	fprintf(stderr, "       -T INT        minimum score to output [%d]\n", passOptions->T);
	fprintf(stderr, "       -h INT[,INT]  if there are <INT hits with score >80%% of the max score, output all in XA [%d,%d]\n", passOptions->max_XA_hits, passOptions->max_XA_hits_alt);
	fprintf(stderr, "       -a            output all alignments for SE or unpaired PE\n");
	fprintf(stderr, "       -C            append FASTA/FASTQ comment to SAM output\n");
	fprintf(stderr, "       -V            output the reference FASTA header in the XR tag\n");
	fprintf(stderr, "       -Y            use soft clipping for supplementary alignments\n");
	fprintf(stderr, "       -M            mark shorter split hits as secondary\n\n");
	fprintf(stderr, "       -I FLOAT[,FLOAT[,INT[,INT]]]\n");
	fprintf(stderr, "                     specify the mean, standard deviation (10%% of the mean if absent), max\n");
	fprintf(stderr, "                     (4 sigma from the mean if absent) and min of the insert size distribution.\n");
	fprintf(stderr, "                     FR orientation only. [inferred]\n");
	fprintf(stderr, "\n");
	fprintf(stderr, "Note: Please read the man page for detailed description of the command line and options.\n");
	fprintf(stderr, "\n");

	return 1;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x10, %rsp
movq %rdi, -0x8(%rbp)
movq 0x36ac5(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e094(%rip), %rsi     # 0x375b1
movb $0x0, %al
callq 0x34e0
movq 0x36aad(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e582(%rip), %rsi     # 0x37ab7
movb $0x0, %al
callq 0x34e0
movq 0x36a95(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e59d(%rip), %rsi     # 0x37aea
movb $0x0, %al
callq 0x34e0
movq 0x36a7d(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e59f(%rip), %rsi     # 0x37b04
movb $0x0, %al
callq 0x34e0
movq 0x36a65(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e5da(%rip), %rsi     # 0x37b57
movb $0x0, %al
callq 0x34e0
movq 0x36a4d(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e612(%rip), %rsi     # 0x37ba7
movb $0x0, %al
callq 0x34e0
movq 0x36a35(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e62e(%rip), %rsi     # 0x37bdb
movb $0x0, %al
callq 0x34e0
movq 0x36a1d(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x68(%rax), %edx
leaq 0x2e670(%rip), %rsi     # 0x37c3c
movb $0x0, %al
callq 0x34e0
movq 0x369fe(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movss 0x6c(%rax), %xmm0
cvtss2sd %xmm0, %xmm0
leaq 0x2e696(%rip), %rsi     # 0x37c87
movb $0x1, %al
callq 0x34e0
movq 0x369d9(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e6d6(%rip), %rsi     # 0x37cdf
movb $0x0, %al
callq 0x34e0
movq 0x369c1(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e70f(%rip), %rsi     # 0x37d30
movb $0x0, %al
callq 0x34e0
movq 0x369a9(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x94(%rax), %edx
leaq 0x2e703(%rip), %rsi     # 0x37d46
movb $0x0, %al
callq 0x34e0
movq 0x36987(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x78(%rax), %edx
leaq 0x2e711(%rip), %rsi     # 0x37d73
movb $0x0, %al
callq 0x34e0
movq 0x36968(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x28(%rax), %edx
leaq 0x2e721(%rip), %rsi     # 0x37da2
movb $0x0, %al
callq 0x34e0
movq 0x36949(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movss 0x84(%rax), %xmm0
cvtss2sd %xmm0, %xmm0
leaq 0x2e72b(%rip), %rsi     # 0x37dd4
movb $0x1, %al
callq 0x34e0
movq 0x36921(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movq 0x30(%rax), %rdx
leaq 0x2e765(%rip), %rsi     # 0x37e2e
movb $0x0, %al
callq 0x34e0
movq 0x36901(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x8c(%rax), %edx
leaq 0x2e789(%rip), %rsi     # 0x37e74
movb $0x0, %al
callq 0x34e0
movq 0x368df(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movss 0xa0(%rax), %xmm0
cvtss2sd %xmm0, %xmm0
leaq 0x2e7a6(%rip), %rsi     # 0x37eb9
movb $0x1, %al
callq 0x34e0
movq 0x368b7(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e7f4(%rip), %rsi     # 0x37f1f
movb $0x0, %al
callq 0x34e0
movq 0x3689f(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0xb8(%rax), %edx
leaq 0x2e81d(%rip), %rsi     # 0x37f6a
movb $0x0, %al
callq 0x34e0
movq 0x3687d(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e859(%rip), %rsi     # 0x37fbe
movb $0x0, %al
callq 0x34e0
movq 0x36865(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e879(%rip), %rsi     # 0x37ff6
movb $0x0, %al
callq 0x34e0
movq 0x3684d(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl (%rax), %edx
leaq 0x2e86f(%rip), %rsi     # 0x3800a
movb $0x0, %al
callq 0x34e0
movq 0x3682f(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x4(%rax), %edx
leaq 0x2e8b7(%rip), %rsi     # 0x38071
movb $0x0, %al
callq 0x34e0
movq 0x36810(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x8(%rax), %edx
movq -0x8(%rbp), %rax
movl 0x10(%rax), %ecx
leaq 0x2e8c3(%rip), %rsi     # 0x380a3
movb $0x0, %al
callq 0x34e0
movq 0x367ea(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0xc(%rax), %edx
movq -0x8(%rbp), %rax
movl 0x14(%rax), %ecx
leaq 0x2e8eb(%rip), %rsi     # 0x380f1
movb $0x0, %al
callq 0x34e0
movq 0x367c4(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x1c(%rax), %edx
movq -0x8(%rbp), %rax
movl 0x20(%rax), %ecx
leaq 0x2e91f(%rip), %rsi     # 0x3814b
movb $0x0, %al
callq 0x34e0
movq 0x3679e(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x18(%rax), %edx
leaq 0x2e942(%rip), %rsi     # 0x3818d
movb $0x0, %al
callq 0x34e0
movq 0x3677f(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e968(%rip), %rsi     # 0x381cb
movb $0x0, %al
callq 0x34e0
movq 0x36767(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e9b0(%rip), %rsi     # 0x3822b
movb $0x0, %al
callq 0x34e0
movq 0x3674f(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2e9f0(%rip), %rsi     # 0x38283
movb $0x0, %al
callq 0x34e0
movq 0x36737(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ea3b(%rip), %rsi     # 0x382e6
movb $0x0, %al
callq 0x34e0
movq 0x3671f(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ea70(%rip), %rsi     # 0x38333
movb $0x0, %al
callq 0x34e0
movq 0x36707(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ea71(%rip), %rsi     # 0x3834c
movb $0x0, %al
callq 0x34e0
movq 0x366ef(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2eacb(%rip), %rsi     # 0x383be
movb $0x0, %al
callq 0x34e0
movq 0x366d7(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2eb02(%rip), %rsi     # 0x3840d
movb $0x0, %al
callq 0x34e0
movq 0x366bf(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2eb4a(%rip), %rsi     # 0x3846d
movb $0x0, %al
callq 0x34e0
movq 0x366a7(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ebac(%rip), %rsi     # 0x384e7
movb $0x0, %al
callq 0x34e0
movq 0x3668f(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x40(%rax), %edx
leaq 0x2ec0c(%rip), %rsi     # 0x38566
movb $0x0, %al
callq 0x34e0
movq 0x36670(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ec52(%rip), %rsi     # 0x385c4
movb $0x0, %al
callq 0x34e0
movq 0x36658(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ec6f(%rip), %rsi     # 0x385f9
movb $0x0, %al
callq 0x34e0
movq 0x36640(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ec9b(%rip), %rsi     # 0x3863d
movb $0x0, %al
callq 0x34e0
movq 0x36628(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ecb5(%rip), %rsi     # 0x3866f
movb $0x0, %al
callq 0x34e0
movq 0x36610(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ece3(%rip), %rsi     # 0x386b5
movb $0x0, %al
callq 0x34e0
movq 0x365f8(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ed07(%rip), %rsi     # 0x386f1
movb $0x0, %al
callq 0x34e0
movq 0x365e0(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ed41(%rip), %rsi     # 0x38743
movb $0x0, %al
callq 0x34e0
movq 0x365c8(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ed88(%rip), %rsi     # 0x387a2
movb $0x0, %al
callq 0x34e0
movq 0x365b0(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2db7f(%rip), %rsi     # 0x375b1
movb $0x0, %al
callq 0x34e0
movq 0x36598(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x373e6(%rip), %rax     # 0x40e30
movl (%rax), %edx
leaq 0x2edb8(%rip), %rsi     # 0x3880b
movb $0x0, %al
callq 0x34e0
movq 0x36577(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0x44(%rax), %edx
leaq 0x2edef(%rip), %rsi     # 0x38861
movb $0x0, %al
callq 0x34e0
movq 0x36558(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
movq -0x8(%rbp), %rax
movl 0xbc(%rax), %edx
movq -0x8(%rbp), %rax
movl 0xc0(%rax), %ecx
leaq 0x2edf6(%rip), %rsi     # 0x38894
movb $0x0, %al
callq 0x34e0
movq 0x3652c(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ee47(%rip), %rsi     # 0x388fd
movb $0x0, %al
callq 0x34e0
movq 0x36514(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ee71(%rip), %rsi     # 0x3893f
movb $0x0, %al
callq 0x34e0
movq 0x364fc(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ee98(%rip), %rsi     # 0x3897e
movb $0x0, %al
callq 0x34e0
movq 0x364e4(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2eec6(%rip), %rsi     # 0x389c4
movb $0x0, %al
callq 0x34e0
movq 0x364cc(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2eef3(%rip), %rsi     # 0x38a09
movb $0x0, %al
callq 0x34e0
movq 0x364b4(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ef17(%rip), %rsi     # 0x38a45
movb $0x0, %al
callq 0x34e0
movq 0x3649c(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ef24(%rip), %rsi     # 0x38a6a
movb $0x0, %al
callq 0x34e0
movq 0x36484(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2ef69(%rip), %rsi     # 0x38ac7
movb $0x0, %al
callq 0x34e0
movq 0x3646c(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2efb2(%rip), %rsi     # 0x38b28
movb $0x0, %al
callq 0x34e0
movq 0x36454(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2da23(%rip), %rsi     # 0x375b1
movb $0x0, %al
callq 0x34e0
movq 0x3643c(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2efb8(%rip), %rsi     # 0x38b5e
movb $0x0, %al
callq 0x34e0
movq 0x36424(%rip), %rax     # 0x3ffd8
movq (%rax), %rdi
leaq 0x2d9f3(%rip), %rsi     # 0x375b1
movb $0x0, %al
callq 0x34e0
movl $0x1, %eax
addq $0x10, %rsp
popq %rbp
retq