// File: /workspace/github_c_makefile_star2_O0/richarddurbin[P]hash10x/moshutils.c
// Function: usage
void usage (void)
{ fprintf (stderr, "Usage: moshutils <commands>\n") ;
  fprintf (stderr, "Commands are executed in order - set parameters before using them!\n") ;
  fprintf (stderr, "  -v | --verbose : toggle verbose mode\n") ;
  fprintf (stderr, "  -o | --output <output filename> : '-' for stdout\n") ;
  fprintf (stderr, "  -c | --moshcreate table_bits{28} kmer{19} window{31} seed{17}: can truncate parameters\n") ;
  fprintf (stderr, "  -r | --read <mosh file>\n") ;
  fprintf (stderr, "  -w | --write <mosh file>\n") ;
  fprintf (stderr, "  -a | --add <read file> : add kmers from read file\n") ;
  fprintf (stderr, "  -x | --add10x <10x read file> : add kmers from 10x read file\n") ;
  fprintf (stderr, "  -m | --merge <mosh file> : add kmers from read file; writes depths\n") ;
  fprintf (stderr, "  -p | --prune <min> <max> : remove mosh entries < min or >= max\n") ;
  fprintf (stderr, "  -s | --setcopy <copy1min> <copy2min> <copyMmin> : reset mosh copy\n") ;
  fprintf (stderr, "  -sM | --setcopyM <copyMmin> : set copyM if depth > copyMmin\n") ;
  fprintf (stderr, "  -H | --hist <outfile> : print depth histogram\n") ;
  fprintf (stderr, "  -d | --depth <outfile> <mosh file>* : print depth per mosh [also in other files]\n") ;
  fprintf (stderr, "command -c or -r must come before other commands from -w onwards\n") ;
  fprintf (stderr, "read files can be fasta or fastq, gzipped or not\n") ;
  fprintf (stderr, "example usage\n") ;
  fprintf (stderr, "  moshutils -c 30 19 31 17 -a XR1.fa.gz -a XR2.fa.gz -w X.mosh\n") ;
  fprintf (stderr, "  moshutils -c 30 19 31 17 -a YR1.fa.gz -a YR2.fa.gz -w Y.mosh\n") ;
  fprintf (stderr, "  moshutils -r X.mosh -m Y.mosh -w XY1.mosh -o XY.his -H\n") ;
  fprintf (stderr, "then look at histogram XY.his and decide on thresholds, then\n") ;
  fprintf (stderr, "  moshutils -r XY1.mosh -p 5 200 -s 10 50 100 -w XY2.mosh\n") ;
  fprintf (stderr, "  moshutils -r XY2.mosh -o XY.depths -d X.mosh Y.mosh\n") ;
  fprintf (stderr, "XY.depths will have columns: hash, depth_in_XY2, depth_inX, depth_in_Y\n") ;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
movq 0xba0d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7a2a(%rip), %rsi      # 0x901f
movb $0x0, %al
callq 0x1120
movq 0xb9f5(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7a2f(%rip), %rsi      # 0x903c
movb $0x0, %al
callq 0x1120
movq 0xb9dd(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7a5b(%rip), %rsi      # 0x9080
movb $0x0, %al
callq 0x1120
movq 0xb9c5(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7a6b(%rip), %rsi      # 0x90a8
movb $0x0, %al
callq 0x1120
movq 0xb9ad(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7a87(%rip), %rsi      # 0x90dc
movb $0x0, %al
callq 0x1120
movq 0xb995(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7ac9(%rip), %rsi      # 0x9136
movb $0x0, %al
callq 0x1120
movq 0xb97d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7acc(%rip), %rsi      # 0x9151
movb $0x0, %al
callq 0x1120
movq 0xb965(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7ad0(%rip), %rsi      # 0x916d
movb $0x0, %al
callq 0x1120
movq 0xb94d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7aed(%rip), %rsi      # 0x91a2
movb $0x0, %al
callq 0x1120
movq 0xb935(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7b15(%rip), %rsi      # 0x91e2
movb $0x0, %al
callq 0x1120
movq 0xb91d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7b43(%rip), %rsi      # 0x9228
movb $0x0, %al
callq 0x1120
movq 0xb905(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7b6d(%rip), %rsi      # 0x926a
movb $0x0, %al
callq 0x1120
movq 0xb8ed(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7b9a(%rip), %rsi      # 0x92af
movb $0x0, %al
callq 0x1120
movq 0xb8d5(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7bc1(%rip), %rsi      # 0x92ee
movb $0x0, %al
callq 0x1120
movq 0xb8bd(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7bda(%rip), %rsi      # 0x931f
movb $0x0, %al
callq 0x1120
movq 0xb8a5(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7c16(%rip), %rsi      # 0x9373
movb $0x0, %al
callq 0x1120
movq 0xb88d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7c40(%rip), %rsi      # 0x93b5
movb $0x0, %al
callq 0x1120
movq 0xb875(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7c5a(%rip), %rsi      # 0x93e7
movb $0x0, %al
callq 0x1120
movq 0xb85d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7c51(%rip), %rsi      # 0x93f6
movb $0x0, %al
callq 0x1120
movq 0xb845(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7c79(%rip), %rsi      # 0x9436
movb $0x0, %al
callq 0x1120
movq 0xb82d(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7ca1(%rip), %rsi      # 0x9476
movb $0x0, %al
callq 0x1120
movq 0xb815(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7cc3(%rip), %rsi      # 0x94b0
movb $0x0, %al
callq 0x1120
movq 0xb7fd(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7ce9(%rip), %rsi      # 0x94ee
movb $0x0, %al
callq 0x1120
movq 0xb7e5(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7d0c(%rip), %rsi      # 0x9529
movb $0x0, %al
callq 0x1120
movq 0xb7cd(%rip), %rax      # 0xcff8
movq (%rax), %rdi
leaq 0x7d2b(%rip), %rsi      # 0x9560
movb $0x0, %al
callq 0x1120
popq %rbp
retq
nop