initial sketch mode stuff

include/AlevinOpts.hpp

@@ -46,8 +46,9 @@ struct AlevinOpts {
   //Stop progress sumps
   bool quiet;
   // just perform alignment and produce 
-  // an output directory with a PAM file. 
+  // an output directory with a RAD file. 
   bool just_align;
+  bool sketch_mode;
   //flag for deduplication
   bool noDedup;
   //flag for not performing external whitelisting

include/SalmonDefaults.hpp

@@ -152,6 +152,7 @@ namespace defaults {
   constexpr const bool noEM{false};
   constexpr const bool debug{true};
   constexpr const bool just_align{false};
+  constexpr const bool sketch_mode{false};
   constexpr const uint32_t trimRight{0};
   constexpr const uint32_t numBootstraps{0};
   constexpr const uint32_t numGibbsSamples{0};

scripts/fetchPufferfish.sh

@@ -23,7 +23,8 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
 fi
 
 #SVER=salmon-v1.3.0
-SVER=develop
+#SVER=develop
+SVER=sketch-mode
 
 EXPECTED_SHA256=0176b2ec5fc45bbf68c60b5845fead28e63db72f91ff93499d67e7a571167fdf
 
@@ -42,7 +43,7 @@ fi
 if [ -z "${hashcheck-}" ]; then
     echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
 else
-    if [[ $SVER != develop ]]; then
+    if [[ $SVER != sketch-mode ]]; then
         echo "${EXPECTED_SHA256}  ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
     else
         echo "not testing sha since pulling from develop"

src/AlevinUtils.cpp

@@ -568,6 +568,7 @@ namespace alevin {
       aopt.jointLog = spdlog::create("alevinLog", std::begin(sinks), std::end(sinks));
 
       aopt.just_align = vm["justAlign"].as<bool>();
+      aopt.sketch_mode = vm["sketchMode"].as<bool>();
       aopt.quiet = vm["quiet"].as<bool>();
       aopt.noEM = vm["noem"].as<bool>();
       aopt.noDedup = vm["noDedup"].as<bool>();
@@ -594,8 +595,18 @@ namespace alevin {
 
       if (aopt.just_align) {
         aopt.jointLog->info("The --justAlign flag was passed to alevin. The "
-        "reads will be selectively aligned and the output written to a PAM file."
+        "reads will be selectively aligned and the output written to a RAD file."
         "Arguments passed that correspond to other processing steps will be ignored");
+        if (aopt.sketch_mode) {
+          aopt.jointLog->info("The --sketchMode flag was passed; the alignment will be run "
+          "in sketch mode.");
+          sopt.mismatchSeedSkip = 15;
+        }
+      } else {
+        if (aopt.sketch_mode) {
+          aopt.jointLog->info("The --sketchMode flag is not meaningful without the "
+          "--justAlign flag.  This flag will be ignored.");
+        }
       }
 
       if (aopt.umiEditDistance > 4 ) {

src/ProgramOptionsGenerator.cpp

@@ -373,8 +373,12 @@ namespace salmon {
       ("help,h", "produce help message")
       ("output,o", po::value<std::string>()->required(), "Output quantification directory.")
       ("justAlign,j", po::bool_switch()->default_value(alevin::defaults::just_align),
-       "just selectively align the data and write the results to a PAM file.  Do not perform "
+       "just selectively align the data and write the results to a RAD file.  Do not perform "
        "the rest of the quantification procedure.")
+      ("sketchMode", po::bool_switch()->default_value(alevin::defaults::sketch_mode),
+       "perform sketching rather than selective alignment and write the results to a RAD file. "
+       "Requires the `--justAlign` flag. Do not perform the rest of the quantification procedure." 
+      )
       ("threads,p",
        po::value<uint32_t>(&(sopt.numThreads))->default_value(sopt.numThreads),
        "The number of threads to use concurrently.")