Add --gencode option to salmon indexer

Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 Add --gencode option to salmon indexer Addresses #15 he commit message for your changes. Lines starting
COMBINE-lab · Aug 18, 2016 · d44df88 · d44df88
1 parent c09fe59
commit d44df88
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/docker/build_test.sh b/docker/build_test.sh
@@ -1,2 +1,2 @@
 #! /bin/bash
-docker build -t combinelab/salmon:0.7.0-pre .
+docker build -t combinelab/salmon:0.7.1-pre .
diff --git a/scripts/fetchRapMap.sh b/scripts/fetchRapMap.sh
@@ -17,10 +17,10 @@ if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
 fi
 
 mkdir -p ${EXTERNAL_DIR}
-curl -k -L https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.7.0.zip -o ${EXTERNAL_DIR}/rapmap.zip
+curl -k -L https://github.com/COMBINE-lab/RapMap/archive/develop-salmon.zip -o ${EXTERNAL_DIR}/rapmap.zip
 rm -fr ${EXTERNAL_DIR}/RapMap
 unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
-mv ${EXTERNAL_DIR}/RapMap-salmon-v0.7.0 ${EXTERNAL_DIR}/RapMap
+mv ${EXTERNAL_DIR}/RapMap-develop-salmon ${EXTERNAL_DIR}/RapMap
 
 mkdir -p ${INSTALL_DIR}/include/rapmap
 mkdir -p ${INSTALL_DIR}/src/rapmap

diff --git a/src/BuildSalmonIndex.cpp b/src/BuildSalmonIndex.cpp
@@ -77,6 +77,7 @@ int salmonIndex(int argc, char* argv[]) {
     uint32_t numThreads;
     bool useQuasi{false};
     bool perfectHash{false};
+    bool gencodeRef{false};
 
     po::options_description generic("Command Line Options");
     generic.add_options()
@@ -86,6 +87,10 @@ int salmonIndex(int argc, char* argv[]) {
     ("kmerLen,k", po::value<uint32_t>(&auxKmerLen)->default_value(31)->required(),
                     "The size of k-mers that should be used for the quasi index.")
     ("index,i", po::value<string>()->required(), "Salmon index.")
+    ("gencode", po::bool_switch(&gencodeRef)->default_value(false), 
+         "This flag will expect the input transcript fasta to be in GENCODE format, and will split "
+         "the transcript name at the first \'|\' character.  These reduced names will be used in the "
+         "output and when looking for these transcripts in a gene to transcript GTF.")
     ("threads,p", po::value<uint32_t>(&numThreads)->default_value(2)->required(),
                             "Number of threads to use (only used for computing bias features)")
     ("perfectHash", po::bool_switch(&perfectHash)->default_value(false), 
@@ -192,6 +197,11 @@ Creates a salmon index.
             if (perfectHash) {
                 argVec->push_back("--perfectHash");
             }
+            if (gencodeRef) {
+                argVec->push_back("-s");
+                argVec->push_back("\"|\"");
+            }
+
             sidx.reset(new SalmonIndex(jointLog, SalmonIndexType::QUASI));
         } else {
             // Build the FMD-based index