fix bug in flag output and quality string reversal

COMBINE-lab · Mar 24, 2016 · 0ec7715 · 0ec7715
1 parent 1375132
commit 0ec7715
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Showing 2 changed files with 56 additions and 14 deletions.
diff --git a/scripts/compile.sh b/scripts/compile.sh
@@ -1,11 +1,45 @@
 #!/bin/bash
 set -e
 
-branch=$1
-version=$2
-cxxflags=$3
+# from http://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash
+no_native_arch=false
+cxxflags=""
+
+while [[ $# > 1 ]]
+do
+    key="$1"
+
+    case $key in
+        -b|--branch)
+            branch="$2"
+            shift # past argument
+            ;;
+        -v|--version)
+            version="$2"
+            shift # past argument
+            ;;
+        -f|--cxxflags)
+            cxxflags="$2"
+            shift # past argument
+            ;;
+        --no-native)
+            no_native_arch=true
+            ;;
+        *)
+            # unknown option
+            ;;
+    esac
+    shift # past argument or value
+done
 
 echo "Building rapmap [branch = ${branch}]. Tagging version as ${version}"
+if [ "$no_native_arch" = true ] ; then 
+    echo "Disabling -march=native"
+fi
+
+if [[ -z $cxxflags ]] ; then
+    echo "Passed CXXFLAGS ${cxxflags}"
+fi
 
 # Activate Holy Build Box environment.
 source /hbb_exe/activate
@@ -27,7 +61,14 @@ mv RapMap-${branch} RapMap
 cd RapMap
 mkdir build
 cd build
-cmake -DFETCH_BOOST=TRUE -DCMAKE_CXX_FLAGS=${cxxflags} ..
+
+
+if [ "$no_native_arch" = true ] ; then 
+    cmake -DFETCH_BOOST=TRUE -DCMAKE_CXX_FLAGS=${cxxflags} -DNO_NATIVE_ARCH ..
+else
+    cmake -DFETCH_BOOST=TRUE -DCMAKE_CXX_FLAGS=${cxxflags} ..
+fi
+
 make
 make install
 make test

diff --git a/src/RapMapUtils.cpp b/src/RapMapUtils.cpp
@@ -58,7 +58,6 @@ namespace rapmap {
             int32_t end = seq.length()-1, start = 0;
             //readWork[end] = '\0';
             //qualWork[end] = '\0';
-            -- end;
             while (LIKELY(start < end)) {
                 readWork[start] = (char)rc_table[(int8_t)seq[end]];
                 readWork[end] = (char)rc_table[(int8_t)seq[start]];
@@ -237,10 +236,9 @@ namespace rapmap {
                     if (qa.isPaired) {
                         rapmap::utils::getSamFlags(qa, true, flags1, flags2);
                         if (alnCtr != 0) {
-                            flags1 |= 0x900; flags2 |= 0x900;
-                        } else {
-                            flags2 |= 0x900;
+                            flags1 |= 0x100; flags2 |= 0x100;
                         }
+
                         rapmap::utils::adjustOverhang(qa, txpLens[qa.tid], cigarStr1, cigarStr2);
 
                         // Reverse complement the read and reverse
@@ -297,17 +295,20 @@ namespace rapmap {
                     } else {
                         rapmap::utils::getSamFlags(qa, true, flags1, flags2);
                         if (alnCtr != 0) {
-                            flags1 |= 0x900; flags2 |= 0x900;
-                        } else {
+                            flags1 |= 0x100; flags2 |= 0x100;
+                        }
+			/*
+			else {
                             // If this is the first alignment for this read
-                            // If the left end is mapped, set 0x900 on the right end
+                            // If the left end is mapped, set 0x100 on the right end
                             if (qa.mateStatus == MateStatus::PAIRED_END_LEFT) {
-                                flags2 |= 0x900;
+                                flags2 |= 0x100;
                             } else {
-                            // Otherwise, set 0x900 on the left end
-                                flags1 |= 0x900;
+                            // Otherwise, set 0x100 on the left end
+                                flags1 |= 0x100;
                             }
                         }
+			*/
 
                         std::string* readSeq{nullptr};
                         std::string* unalignedSeq{nullptr};