update storage type for tag slices

COMBINE-lab · Oct 9, 2020 · e01a7c2 · e01a7c2
1 parent 19d66ca
commit e01a7c2
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Showing 2 changed files with 15 additions and 7 deletions.
diff --git a/include/SingleCellProtocols.hpp b/include/SingleCellProtocols.hpp
@@ -6,14 +6,17 @@
 
 #include "AlevinOpts.hpp"
 #include "AlevinTypes.hpp"
-#include "pufferfish/chobo/small_vector.hpp"
+#include "pufferfish/chobo/static_vector.hpp"
 
 namespace alevin{
   namespace protocols {
 
+    static constexpr size_t num_tag_pieces{16};
     struct TagGeometry {
       uint32_t read_num{0};
-      std::vector<std::pair<uint32_t, uint32_t>> substr_locs{};
+      chobo::static_vector<std::pair<uint32_t, uint32_t>, num_tag_pieces> substr_locs{};
+      // chobo::static_vector<std::pair<uint32_t,uint8_t>, 16> bc_locs;
+      // std::vector<std::pair<uint32_t, uint32_t>> substr_locs{};
       uint32_t length{0};
       uint32_t largest_index{0};
 
@@ -119,8 +122,6 @@ namespace alevin{
       // vector of offset, length pairs
       TagGeometry umi_geo;
       TagGeometry bc_geo;
-      //chobo::static_vector<std::pair<uint32_t,uint8_t>, 16> umi_locs;
-      //chobo::static_vector<std::pair<uint32_t,uint8_t>, 16> bc_locs;
 
       void set_umi_geo(TagGeometry& g) { umi_geo = g; umiLength = umi_geo.length; };
       void set_bc_geo(TagGeometry& g) { bc_geo = g; barcodeLength = bc_geo.length; };

diff --git a/src/AlevinUtils.cpp b/src/AlevinUtils.cpp
@@ -521,9 +521,9 @@ namespace alevin {
       d.clear();
       if ( parser.parse(geo_string.c_str()) ) {
         if (d.size() > 1) {
-          //aopt.jointLog->error("Though supported in the syntax, the current implementation \n"
-          //                     "of custom tag geometry does not support having a tag \n"
-          //                     "split over more than one read.");    
+          log->error("Though supported in the syntax, the current implementation \n"
+                     "of custom tag geometry does not support having a tag \n"
+                     "split over more than one read.");    
           return false;
         }
 
@@ -545,6 +545,13 @@ namespace alevin {
           if (stop < start) { return false; }
           int len = (stop - start) + 1;
           tlen += len;
+          if (tg.substr_locs.size() >= alevin::protocols::num_tag_pieces) {
+            log->error("Currently, alevin does not support the tag (barcode / umi) being "
+                       "split into more than {} pieces.  If the current bound is a "
+                       "problem for your protocol, please reach out on GitHub.",
+                       alevin::protocols::num_tag_pieces);
+            return false;
+          }
           tg.substr_locs.push_back(std::make_pair(static_cast<uint32_t>(start), static_cast<uint32_t>(len)));
         }
         tg.length = tlen;