format-analysis: positions start at 1 in seg

There were some discrepancies that made the situation ambiguous.
Now we clearly state that positions must start at 1.

The code is updated accordingly.

browser/js/clone.js

@@ -145,7 +145,7 @@ Clone.prototype = {
     getSegNtSequence: function(field_name) {
         positions = this.getSegStartStop(field_name)
         if (positions != null) {
-            return this.sequence.substr(positions['start'], positions['stop'] - positions['start']+1)
+            return this.sequence.substr(positions['start']-1, positions['stop'] - positions['start']+1)
         }
         return '';
     },

browser/test/QUnit/testFiles/clone_test.js

@@ -189,7 +189,7 @@ test('clone: get info from seg', function() {
     equal(pos_junction['start'], 9, "start junction of c1")
     equal(pos_junction['stop'], 11, "stop junction of c1")
 
-    equal(c1.getSegNtSequence('junction'), 'att', 'junction c1')
+    equal(c1.getSegNtSequence('junction'), 'aat', 'junction c1')
     equal(c1.getSegAASequence('junction'), '', 'no AA junction for c1')
     equal(c1.getSegAASequence('cdr3'), 'ABCDE', 'AA CDR3 for c1')
 });

doc/format-analysis.org

@@ -279,6 +279,7 @@ In the .analysis file, this section is intended to describe some specific clones
                      // in the browser clones, that are not segmented will be shown on the grid with '?/?'
                      // positions are related to the 'sequence'
                      // names of V/D/J genes should match the ones in files referenced in germline/germline.data
+                     // Positions must start at 1.
       {
          "5": "IGHV5*01",
          "5start": 0, 
@@ -297,8 +298,9 @@ In the .analysis file, this section is intended to describe some specific clones
                      // CDR3 should be stored that way (in a field called "cdr3"), this is similar
                      // for the other region of interest.
                      // The junction is also stored in that way (in a "junction" field),
-                     // its productivity must be stored in a boolean field called "productive"
-         "somefeature": { "start": 0, "stop": 0, "seq": "" }
+                     // its productivity must be stored in a boolean field called "productive".
+                     // Positions must also start at 1.
+         "somefeature": { "start": 1, "stop": 100, "seq": "" }
       }