minor changes

flank_detector.cpp

@@ -297,6 +297,8 @@ std::string FlankDetector::shift_str(std::string& seq, uint32_t i)
 
 /**
  * Score a string based on complete alignment.
+ * This is for the purpose of computing a motif score.
+ * It might make sense to incorporate alignment in a limited sense.
  */
 int32_t FlankDetector::compute_score(int32_t start, int32_t len, std::string& a, std::string& b)
 {    

flank_detector.h

@@ -105,17 +105,6 @@ class FlankDetector
      */
     ~FlankDetector();
 
-//    /**
-//     * Computes purity score of a sequence with respect to a motif.
-//     */
-//    void compute_purity_score(Variant& variant, int32_t amode);
-//
-//    /**
-//     * Computes purity score of a sequence with respect to a motif.
-//     */
-//    void detect_flanks(std::string& repeat_tract, std::string& motif);
-//        
-
     /**
      * Detect repeat region.
      */
@@ -127,10 +116,12 @@ class FlankDetector
     std::string shift_str(std::string& seq, uint32_t i);
 
     /**
-     * Score string.
+     * Score a string based on complete alignment.
+     * This is for the purpose of computing a motif score.
+     * It might make sense to incorporate alignment in a limited sense.
      */
     int32_t compute_score(int32_t start, int32_t len, std::string& a, std::string& b);
-        
+
     /**
      * Chooses a phase of the motif that is appropriate for the alignment from the 5 prime end.
      * This differs from choose_exact_repeat_unit() where the motif is returned
@@ -140,10 +131,10 @@ class FlankDetector
 
     /**
      * Chooses a phase of the motif that is appropriate for the alignment from the 5 prime end.
-     * If no exact match is available, the best possible match is returned. 
+     * If no exact match is available, the best possible match is returned.
      */
     std::string choose_fuzzy_5prime_repeat_unit(std::string& seq, std::string& motif);
-            
+
     /**
      * Chooses a phase of the motif that is appropriate for the alignment from the 3 prime end.
      * This differs from choose_exact_repeat_unit() where the motif is returned
@@ -153,10 +144,10 @@ class FlankDetector
 
     /**
      * Chooses a phase of the motif that is appropriate for the alignment from the 3 prime end.
-     * If no exact match is available, the best possible match is returned. 
+     * If no exact match is available, the best possible match is returned.
      */
     std::string choose_fuzzy_3prime_repeat_unit(std::string& seq, std::string& motif);
-    
+
     /**
      * Chooses a phase of the motif that is appropriate for the alignment.
      * This returns the empty string if the motif does not have an exact
@@ -183,7 +174,7 @@ class FlankDetector
      * Computes purity score of a sequence with respect to a motif.
      */
     void compute_purity_score(std::string& repeat_tract, std::string& motif);
-    
+
     /**
     * Computes composition and entropy of repeat tract.
     */

lib/htslib/tabix.1

@@ -69,10 +69,14 @@ sorted and compressed by
 .B bgzip
 which has a
 .BR gzip (1)
-like interface. After indexing, tabix is able to quickly retrieve data
-lines overlapping
+like interface.
+
+After indexing, tabix is able to quickly retrieve data lines overlapping
 .I regions
-specified in the format "chr:beginPos-endPos". Fast data retrieval also
+specified in the format "chr:beginPos-endPos".
+(Coordinates specified in this region format are 1-based and inclusive.)
+
+Fast data retrieval also
 works over network if URI is given as a file name and in this case the
 index file will be downloaded if it is not present locally.
 
@@ -98,7 +102,7 @@ start column. [5]
 .B "-f, --force "
 Force to overwrite the index file if it is present.
 .TP
-.BI "-m, --min-shift" INT
+.BI "-m, --min-shift " INT
 set minimal interval size for CSI indices to 2^INT [14]
 .TP
 .BI "-p, --preset " STR