patch to htgt/CRISPR-Analyser

ots_server.patch

diff --git a/src/crisprutil.cpp b/src/crisprutil.cpp
index 91d9b4c..0480e27 100644
--- a/src/crisprutil.cpp
+++ b/src/crisprutil.cpp
@@ -44,6 +44,10 @@ void CrisprUtil::_populate_cmap() {
 string CrisprUtil::get_crispr(uint64_t id) {
     return util::bits_to_string( get_crispr_int(id), crispr_data.seq_length );
 }
+// 2014-9-9 : id with offset need to be correct
+string CrisprUtil::get_offset_crispr(uint64_t id) {
+    return util::bits_to_string( get_crispr_int(id - crispr_data.offset), crispr_data.seq_length );
+}
 
 uint64_t CrisprUtil::get_crispr_int(uint64_t id) {
     //make sure load_binary has been called
diff --git a/src/crisprutil.h b/src/crisprutil.h
index aaf1498..939c99e 100644
--- a/src/crisprutil.h
+++ b/src/crisprutil.h
@@ -55,6 +55,7 @@ class CrisprUtil {
         uint8_t cmap[256];
         void load_binary(const std::string & outfile);
         std::string get_crispr(uint64_t id);
+        std::string get_offset_crispr(uint64_t id);
         uint64_t get_crispr_int(uint64_t id);
         uint64_t num_seqs();
         uint64_t seq_length();
diff --git a/src/ots_server.cpp b/src/ots_server.cpp
index 12f6d93..6a194e4 100644
--- a/src/ots_server.cpp
+++ b/src/ots_server.cpp
@@ -146,6 +146,10 @@ protected:
                         result = search_json(request);
                         res = true;
                     }
+                    else if ( uri == string("/api/id") ) {
+                        result = id_json(request);
+                        res = true;
+                    }
                     else if ( uri == string("/api/off_targets") ) {
                         result = find_off_targets(request);
                         res = true;
@@ -193,6 +197,8 @@ protected:
         response.setConnectionAlive(false);
         response.setCacheDisabled();
         response.setContentType(content_type);
+        response.setHeaderValue("Access-Control-Allow-Origin", "*");
+        response.setHeaderValue("Cache-Control", "no-cache, must-revalidate");
         response.addContent(result);
         response.write();
     }
@@ -260,6 +266,28 @@ protected:
         return util::to_json_array(matches);
     }
 
+    const string id_json(const MongooseRequest& request) {
+        vector<string> seqs;
+        string ids_text;
+        request.getVar("ids", ids_text);
+        string species;
+        request.getVar("species", species);
+
+        if ( ids_text.empty() )
+            throw runtime_error("Please provide ids");
+        if ( species.empty() )
+            throw runtime_error("Please provide a species");
+
+        util::lc(species);
+        vector<string> ids = util::split(ids_text);
+
+        for ( uint64_t i = 0; i < ids.size(); i++ ) {
+            seqs.push_back( "'" + get_util(species)->get_offset_crispr( stoull(ids[i]) ) + "'" );
+        }
+
+        return util::to_json_array(seqs);
+    }
+
     const string find_off_targets(const MongooseRequest& request) {
         string species;
         string result = "{";
@@ -320,7 +348,7 @@ protected:
 int usage() {
     fprintf(stderr, "\n");
     fprintf(stderr, "Program: ots_server\n");
-    fprintf(stderr, "Contact: Alex Hodgkins <ah19@sanger.ac.uk>\n");
+    fprintf(stderr, "Contact: Alex Hodgkins <ah19@sanger.ac.uk>, Liang Cai\n");
     fprintf(stderr, "Description: A server version of the crispr_analyser that responds to JSON requests\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Usage: ots_server [options]\n");
@@ -329,7 +357,8 @@ int usage() {
     fprintf(stderr, "         -p INT     The port to run the server on\n");
     fprintf(stderr, "         -l FILE    The file containing the human CRISPR index\n");
     fprintf(stderr, "         -m FILE    The file containing the mouse CRISPR index\n");
-    fprintf(stderr, "         -s         Load the default mouse/crispr indexes (sanger only)\n");
+    fprintf(stderr, "         -g FILE    The file containing the dog CRISPR index\n");
+    fprintf(stderr, "         -s         Load the default mouse/crispr indexes (fb.actin only)\n");
     fprintf(stderr, "         -d         Daemon mode\n");
     fprintf(stderr, "\n");
 
@@ -342,14 +371,15 @@ int main(int argc, char * argv[]) {
 
     bool default_opts = false;
     bool daemon = false;
-    string human_index, mouse_index;
+    string human_index, mouse_index, dog_index;
     int c = -1;
-    while ( (c = getopt(argc, argv, "t:p:l:m:sd")) != -1 ) {
+    while ( (c = getopt(argc, argv, "t:p:l:m:g:sd")) != -1 ) {
         switch ( c ) {
             case 't': num_threads  = optarg; break;
             case 'p': port         = optarg; break;
             case 'l': human_index  = optarg; break;
             case 'm': mouse_index  = optarg; break;
+            case 'g': dog_index  = optarg; break;
             case 's': default_opts = true; break;
             case 'd': daemon       = true; break;
             case '?': return usage();
@@ -357,12 +387,13 @@ int main(int argc, char * argv[]) {
     }
 
     if ( default_opts ) {
-        human_index = "/lustre/scratch109/sanger/team87/crispr_indexes/GRCh37_index.bin";
-        mouse_index = "/lustre/scratch109/sanger/team87/crispr_indexes/GRCm38_index.bin";
+        human_index = "/home/liang/crisprs_human.bin";
+        mouse_index = "/home/liang/crisprs_mouse.bin";
+        dog_index = "/home/liang/crisprs_cf3.bin";
     }
     else { 
-        if ( human_index.empty() && mouse_index.empty() ) {
-            cerr << "You must specify at least 1 index to load, or use -s to use the default indexes in /lustre" << endl;
+        if ( human_index.empty() && mouse_index.empty() && dog_index.empty() ) {
+            cerr << "You must specify at least 1 index to load, or use -s to use the default indexes" << endl;
             return usage();
         }
     }
@@ -397,6 +428,7 @@ int main(int argc, char * argv[]) {
 
     if ( ! human_index.empty() ) server.load_index("human", human_index);
     if ( ! mouse_index.empty() ) server.load_index("mouse", mouse_index);
+    if ( ! dog_index.empty() ) server.load_index("dog", dog_index);
 
     server.setOption("document_root", "html");
     server.setOption("listening_ports", port);

ots_server has jsonp support
the following is not required
Access-Control-Allow-Origin "*"