24.12.29 README updated

README.md

@@ -28,7 +28,7 @@ Examples
 
 * Example:
 
-        teloscope -f "${file}" -o "${out_path}" -j 16 -c TTAGGG -p TBAGGG,TTRGGG,YTAGGG  -w 2000 -s 1000 -d 200 -l 1000 -r -g -e -m -i  --verbose
+        teloscope -f "${file}" -o "${out_path}" -j 16 -c TTAGGG -p TBAGGG,TTRGGG,YTAGGG  -w 2000 -s 1000 -d 200 -l 1000 -r -g -e -m -i -t 50000 --verbose
 
 **Note:** Teloscope accepts nucleotides in IUPAC format and generates all possible pattern combinations. 
 
@@ -47,8 +47,9 @@ Required Parameters:
         '-w'    --window        Set sliding window size. [Default: 1000]
         '-s'    --step  Set sliding window step. [Default: 500]
         '-j'    --threads       Set maximum number of threads. [Default: max. available]
-        '-l'    --min-block-length      Set minimum block length for merging. [Default: 1000]
-        '-d'    --max-block-distance    Set maximum block distance for merging. [Default: 200]
+        '-l'    --min-block-length      Set minimum block length for merging. [Default: 500]
+        '-d'    --max-block-distance    Set maximum block distance for merging. [Default: 50]
+        '-t'    --terminal-limit        Set terminal limit for exploring telomere variant regions (TVRs). [Default: 50000]
 
 Optional Parameters:
         '-r'    --out-win-repeats       Output canonical/noncanonical repeats and density by window. [Default: false]

include/input.h

@@ -15,7 +15,7 @@ struct UserInputTeloscope : UserInput {
     uint32_t windowSize = 1000;
     uint8_t kmerLen = 21;
     uint32_t step = 500;
-    unsigned short int minBlockLen = 1000; // Only for all blocks
+    unsigned short int minBlockLen = 500; // Only for all blocks
     unsigned short int maxBlockDist = 200;
     unsigned short int minBlockCounts = 2;
     uint32_t terminalLimit = 50000;

src/main.cpp

@@ -2,7 +2,7 @@
 #include <input.h> // check
 
 
-std::string version = "0.0.5";
+std::string version = "0.0.6";
 
 // global
 std::chrono::high_resolution_clock::time_point start = std::chrono::high_resolution_clock::now();