update the readme and some help messages

README.md

@@ -1,6 +1,6 @@
 # sigtk
 
-A simple toolkit written for performing various operations on nanopore raw signal data. This is still in a very premature development stage and thus anticipate changes. Currently, *sigtk* is single threaded and has not been optimised for performance. The intended use is to perform operations on relatively smaller datasets for learning purposes and eyeballing.
+A simple toolkit written for performing various operations on nanopore raw signal data.  *sigtk* is single threaded and is not optimised for performance. The intended use is to perform operations on relatively smaller datasets for learning purposes and eyeballing.
 
 ## Building
 
@@ -105,14 +105,9 @@ Prints signal statistics.
 |7  |int   |raw_median      |Median of raw signal values                                            |
 |8  |float |pa_median       |Mean of pico-amperes scaled signal                                     |
 
-
-## subtools under development
-
-Note that these are not much tested and the interface and output may change at anytime.
-
 ### prefix
 
-Under construction. Will change anytime. Only for direct RNA at the moment.
+Under development. Only for direct RNA at the moment.
 Finds prefix segments in a raw signal such as adaptor and polyA.
 
 |Col|Type  |Name            |Description                                                            |
@@ -137,7 +132,7 @@ If `--print-stat` is printed, following additional columns will be printed.
 
 ### jnn
 
-Under construction. Will change anytime. Print segments found using JNN segmenter.
+Under development.  Print segments found using JNN segmenter.
 
 |Col|Type  |Name            |Description                                                            |
 |--:|:----:|:------:        |:-----------------------------------------                             |
@@ -163,9 +158,20 @@ If `-c` is specified, output will be in the following short notation by using re
 
 `100H10,91H11,`
 
+
+### ss
+
+Under development. Operations to convert to/from signal alignment string (ss). See https://hasindu2008.github.io/f5c/docs/output#resquiggle-paf-output-format for explanation of ss.
+
+To convert a PAF file with ss tags to TSV, you can use:
+```
+sigtk ss paf2tsv in.paf
+```
+
+
 ### ent
 
-Under construction. Will change anytime. Calculates shannon entropy for reads in a given S/BLOW5 file.
+Calculates shannon entropy for reads in a given S/BLOW5 file.
 
 |Col|Type  |Name            |Description                                                            |
 |--:|:----:|:------:        |:-----------------------------------------                             |
@@ -174,25 +180,18 @@ Under construction. Will change anytime. Calculates shannon entropy for reads in
 |3  |float   |delta_ent     |entropy after zig-zag delta                                  |
 |4  |float   |byte_ent       |entropy after splitting and storing least significant byte and most significant byte of the zig-zag delta values separately: ent(LSB)+ent(MSB)                                    |
 
-### ss
-
-Under construction. Will change anytime. Operations to convert to/from signal alignment string (ss). See https://hasindu2008.github.io/f5c/docs/output#resquiggle-paf-output-format for explanation of ss.
-
-To convert a PAF file with ss tags to TSV, you can use:
-```
-sigtk ss paf2tsv in.paf
-```
-
 ### qts
-Under construction. Will change anytime. Quantise the raw signal in a S/BLOW5 files. Takes a S/BLOW5 file as the input and writes the quantised output to a S/BLOW5 file.
+
+Quantise the raw signal in a S/BLOW5 files. Takes a S/BLOW5 file as the input and writes the quantised output to a S/BLOW5 file.
 
 Usage:
 ```
 sigtk qts original.blow5 -o quantised.blow5
 ```
 
 Options:
-`-q INT` : Number of LSB bits to trucate (set to 0). Default is 1.
+`-q INT` : Number of lower significant bits eliminate. Default is 1.
+`-m [floor|round|fill-ones]`: quantisation method. Default is round.
 
 
 ## Acknowledgement

src/main.c

@@ -58,7 +58,7 @@ int print_usage(FILE *fp_help){
     fprintf(fp_help,"         jnn       print segments found using JNN segmenter\n");
     fprintf(fp_help,"         ss        ss string conversion\n");
     fprintf(fp_help,"         ent       calculate entropies\n");
-    fprintf(fp_help,"         qts       quantise\n");
+    fprintf(fp_help,"         qts       quantise the raw signal in a S/BLOW5 files\n");
 
     if(fp_help==stderr){
         exit(EXIT_FAILURE);

src/qts.c

@@ -27,13 +27,13 @@ static struct option long_options[] = {
 int round_to_power_of_2(int number, int number_of_bits) {
     //create a binary mask with the specified number of bits
     int bit_mask = (1 << number_of_bits) - 1;
-    
+
     //extract out the value of the LSBs considered
     int lsb_bits = number & bit_mask;
-    
-     
+
+
     int round_threshold = (1 << (number_of_bits - 1));
-    
+
     //check if the least significant bits are closer to 0 or 2^n
     if (lsb_bits < round_threshold) {
         return (number & ~bit_mask) + 0; //round down to the nearest power of 2
@@ -46,7 +46,7 @@ int round_to_power_of_2(int number, int number_of_bits) {
 
 int qtsmain(int argc, char* argv[]) {
 
-    const char* optstring = "hVv:o:b:";
+    const char* optstring = "hVv:o:b:m:";
 
     int longindex = 0;
     int32_t c = -1;
@@ -56,7 +56,7 @@ int qtsmain(int argc, char* argv[]) {
 
     int8_t b = 1; //number of LSB bits to truncate
 
-    char *method = "floor"; //quantization method
+    char *method = "round"; //quantization method
 
     //parse the user args
     while ((c = getopt_long(argc, argv, optstring, long_options, &longindex)) >= 0) {
@@ -67,10 +67,10 @@ int qtsmain(int argc, char* argv[]) {
             fp_help = stdout;
         } else if (c=='o'){
             out_fn = optarg;
-        } else if (c=='b'){  
+        } else if (c=='b'){
             b = atoi(optarg);
-            if (b < 0 || b > 16) {
-                fprintf(stderr, "Error: number of bits to truncate must be between 0 and 8\n");
+            if (b < 1 || b > 8) {
+                fprintf(stderr, "Error: number of bits to truncate must be between 1 and 8\n");
                 exit(EXIT_FAILURE);
             }
         } else if (c=='m'){
@@ -84,8 +84,8 @@ int qtsmain(int argc, char* argv[]) {
         fprintf(fp_help,"   -h                            help\n");
         fprintf(fp_help,"   -o FILE                       output file\n");
         fprintf(fp_help,"   --version                     print version\n");
-        fprintf(fp_help,"   -b INT                        number of LSB bits to truncate [%d]\n", b);
-        fprintf(fp_help,"   --method=[floor|round|fill-ones]   quantization method\n");
+        fprintf(fp_help,"   -b INT                        number of lower significant bits to eliminate [%d]\n", b);
+        fprintf(fp_help,"   -m [floor|round|fill-ones]    quantisation method [round]\n");
         if(fp_help == stdout){
             exit(EXIT_SUCCESS);
         }
@@ -140,7 +140,7 @@ int qtsmain(int argc, char* argv[]) {
             fprintf(stderr,"Unknown method for -m. Available options are floor,round,fill-ones.\n");
             exit(EXIT_FAILURE);
         }
-        
+
         //write to file
         if(slow5_write(rec, sp_w) < 0){
             fprintf(stderr,"Error writing record!\n");