update help message

src/meth_main.c

@@ -482,6 +482,7 @@ int meth_main(int argc, char* argv[], int8_t mode) {
  fprintf(fp_help," -x STR parameter profile to be used for better performance (always applied before other options)\n"); //Added option in help
  fprintf(fp_help," e.g., laptop, desktop, hpc; see https://f5c.page.link/profiles for the full list\n");
  fprintf(fp_help," --iop INT number of I/O processes to read fast5 files [%d]\n",opt.num_iop);
+ fprintf(fp_help," --pore STR set the pore chemistry (r9 or r10) [r9]\n");
  fprintf(fp_help," --slow5 FILE read from a slow5 file\n");
  fprintf(fp_help," --min-mapq INT minimum mapping quality [%d]\n",opt.min_mapq);
  fprintf(fp_help," --secondary=yes|no consider secondary mappings or not [%s]\n",(opt.flag&F5C_SECONDARY_YES)?"yes":"no");
@@ -505,19 +506,19 @@ int meth_main(int argc, char* argv[], int8_t mode) {
  fprintf(fp_help," --meth-out-version INT methylation tsv output version (set 2 to print the strand column) [%d]\n",opt.meth_out_version);
  }
  if(mode==1){
- fprintf(fp_help," -c output in PAF format\n");
  fprintf(fp_help," --summary FILE summarise the alignment of each read/strand in FILE\n");
+ fprintf(fp_help," --paf write output in PAF format\n");
  fprintf(fp_help," --sam write output in SAM format\n");
+ fprintf(fp_help," --sam-out-version INT sam output version (set 1 to revert to old nanopolish style format) [%d]\n",opt.meth_out_version);
+
  fprintf(fp_help," --print-read-names print read names instead of indexes\n");
  fprintf(fp_help," --scale-events scale events to the model, rather than vice-versa\n");
  fprintf(fp_help," --samples write the raw samples for the event to the tsv output\n");
  fprintf(fp_help," --signal-index write the raw signal start and end index values for the event to the tsv output\n");
  fprintf(fp_help," --rna the dataset is direct RNA\n");
  fprintf(fp_help," --collapse-events collapse events that stays on the same reference k-mer\n");
- fprintf(fp_help," --sam-out-version INT sam output version (set 1 to rever to old nanopolish style format) [%d]\n",opt.meth_out_version);
  }
  fprintf(fp_help," --min-recalib-events INT minimum number of events to recalbrate (decrease if your reads are very short and could not calibrate) [%d]\n",opt.min_num_events_to_rescale);
- fprintf(fp_help," --pore STR r9 or r10\n");
 
 #ifdef HAVE_CUDA
  fprintf(fp_help," --cuda-mem-frac FLOAT Fraction of free GPU memory to allocate [0.9 (0.7 for tegra)]\n");