use local protocol, convert from chobo to itlib

COMBINE-lab · Jan 22, 2022 · 7674ea3 · 7674ea3
1 parent 575a2fe
commit 7674ea3
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Showing 4 changed files with 11 additions and 12 deletions.
diff --git a/include/SalmonMappingUtils.hpp b/include/SalmonMappingUtils.hpp
@@ -56,7 +56,7 @@
 #include "pufferfish/ksw2pp/KSW2Aligner.hpp"
 #include "pufferfish/metro/metrohash64.h"
 #include "pufferfish/SelectiveAlignmentUtils.hpp"
-#include "pufferfish/chobo/small_vector.hpp"
+#include "pufferfish/itlib/small_vector.hpp"
 #include "parallel_hashmap/phmap.h"
 
 namespace salmon {
@@ -122,7 +122,7 @@ namespace salmon {
       int32_t secondBestScore;
       int32_t bestDecoyScore;
       double decoyThresh;
-      chobo::small_vector<std::pair<int32_t, int32_t>> best_decoy_hits;
+      itlib::small_vector<std::pair<int32_t, int32_t>> best_decoy_hits;
       bool collect_decoy_info_;
       std::vector<int32_t> scores_;
       phmap::flat_hash_map<uint32_t, std::pair<int32_t, int32_t>> bestScorePerTranscript_;

diff --git a/include/SingleCellProtocols.hpp b/include/SingleCellProtocols.hpp
@@ -6,7 +6,7 @@
 
 #include "AlevinOpts.hpp"
 #include "AlevinTypes.hpp"
-#include "pufferfish/chobo/static_vector.hpp"
+#include "pufferfish/itlib/static_vector.hpp"
 
 namespace alevin{
   namespace protocols {
@@ -15,8 +15,8 @@ namespace alevin{
     struct TagGeometry {
       // uint32_t read_num{0};
       // tuples are read_num, start_pos, length
-      chobo::static_vector<std::pair<uint32_t, size_t>, num_tag_pieces> substr_locs1{};
-      chobo::static_vector<std::pair<uint32_t, size_t>, num_tag_pieces> substr_locs2{};
+      itlib::static_vector<std::pair<uint32_t, size_t>, num_tag_pieces> substr_locs1{};
+      itlib::static_vector<std::pair<uint32_t, size_t>, num_tag_pieces> substr_locs2{};
       // the total length of the tag on read 1 
       size_t length1{0};
       // the total length of the tag on read 2

diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
@@ -89,7 +89,7 @@ cp -r ${EXTERNAL_DIR}/pufferfish/include/libdivide ${INSTALL_DIR}/include/puffer
 cp -r ${EXTERNAL_DIR}/pufferfish/include/ksw2pp ${INSTALL_DIR}/include/pufferfish
 cp -r ${EXTERNAL_DIR}/pufferfish/include/compact_vector ${INSTALL_DIR}/include/pufferfish
 cp -r ${EXTERNAL_DIR}/pufferfish/include/metro ${INSTALL_DIR}/include/pufferfish
-cp -r ${EXTERNAL_DIR}/pufferfish/include/chobo ${INSTALL_DIR}/include/pufferfish
+cp -r ${EXTERNAL_DIR}/pufferfish/include/itlib ${INSTALL_DIR}/include/pufferfish
 cp -r ${EXTERNAL_DIR}/pufferfish/include/sparsepp ${INSTALL_DIR}/include/pufferfish
 cp -r ${EXTERNAL_DIR}/pufferfish/include/simde ${INSTALL_DIR}/include/pufferfish
 cp -r ${EXTERNAL_DIR}/pufferfish/include/tsl ${INSTALL_DIR}/include/pufferfish
@@ -116,7 +116,7 @@ cp ${EXTERNAL_DIR}/pufferfish/src/rank9b.cpp ${INSTALL_DIR}/src/pufferfish
 #cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap
 #cp -r ${EXTERNAL_DIR}/RapMap/include/sparsepp ${INSTALL_DIR}/include/rapmap
 #cp -r ${EXTERNAL_DIR}/RapMap/include/digestpp ${INSTALL_DIR}/include/rapmap
-#cp -r ${EXTERNAL_DIR}/RapMap/include/chobo ${INSTALL_DIR}/include/rapmap
+#cp -r ${EXTERNAL_DIR}/RapMap/include/itlib ${INSTALL_DIR}/include/rapmap
 #cp -r ${EXTERNAL_DIR}/RapMap/include/metro ${INSTALL_DIR}/include/rapmap
 #cp -r ${EXTERNAL_DIR}/RapMap/include/ksw2pp ${INSTALL_DIR}/include/rapmap
 #cp -r ${EXTERNAL_DIR}/RapMap/include/tsl ${INSTALL_DIR}/include/rapmap

diff --git a/src/SalmonAlevin.cpp b/src/SalmonAlevin.cpp
@@ -131,7 +131,7 @@
 #include "pufferfish/ksw2pp/KSW2Aligner.hpp"
 #include "pufferfish/metro/metrohash64.h"
 #include "parallel_hashmap/phmap.h"
-#include "pufferfish/chobo/static_vector.hpp"
+#include "pufferfish/itlib/static_vector.hpp"
 #include "pufferfish/SelectiveAlignmentUtils.hpp"
 
 namespace alevin{
@@ -717,7 +717,7 @@ void process_reads_sc_sketch(paired_parser* parser, ReadExperimentT& readExp, Re
             if (isUmiIdxOk) {
               jointHitGroup.setUMI(umiIdx.word(0));
               bool rh = false;
-              std::string* readSubSeq = aut::getReadSequence(alevinOpts.protocol, rp.first.seq, rp.second.seq, readBuffer);
+              std::string* readSubSeq = aut::getReadSequence(localProtocol, rp.first.seq, rp.second.seq, readBuffer);
               rh = tooShortRight
                        ? false
                        : memCollector.get_raw_hits_sketch(*readSubSeq,
@@ -1242,8 +1242,7 @@ void process_reads_sc_align(paired_parser* parser, ReadExperimentT& readExp, Rea
                 }
               } else {
                 */
-              readSubSeq = aut::getReadSequence(
-                  alevinOpts.protocol, rp.first.seq, rp.second.seq, readBuffer);
+              readSubSeq = aut::getReadSequence(localProtocol, rp.first.seq, rp.second.seq, readBuffer);
               auto rh = tooShortRight ? false
                                       : memCollector(*readSubSeq, qc,
                                                      true, // isLeft
@@ -1756,7 +1755,7 @@ void processReadsQuasi(
                 }
               } else {
               */
-              readSubSeq = aut::getReadSequence(alevinOpts.protocol, rp.first.seq, rp.second.seq, readBuffer);
+              readSubSeq = aut::getReadSequence(localProtocol, rp.first.seq, rp.second.seq, readBuffer);
               auto rh = tooShortRight ? false
                                       : memCollector(*readSubSeq, qc,
                                                      true, // isLeft