Merge pull request #125 from cancerit/dev

merge for hotfix release

.gitignore

@@ -6,3 +6,5 @@
 setup.log
 /tests/*.dSYM
 /install
+debug-scratch/
+install_tmp/

CHANGES.md

@@ -1,5 +1,10 @@
 # CHANGES
 
+## 1.15.5
+
+* Fix memory bug in split
+* Add debug option to setup.sh and Makefile
+
 ## 1.15.4
 
 * Fix memory bug causing crash in generateCavemanUMNormVCF

Makefile

@@ -1,9 +1,8 @@
-CAVEMAN_VERSION=1.15.4
+CAVEMAN_VERSION=1.15.5
 
 TEST_REF?=""
 #Compiler
-CC?=gcc
-CC+= -O3 -g -DCAVEMAN_VERSION='"$(CAVEMAN_VERSION)"' -DTEST_REF='"$(TEST_REF)"'
+CC = gcc -DCAVEMAN_VERSION='"$(CAVEMAN_VERSION)"' -DTEST_REF='"$(TEST_REF)"'
 
 #debug compiler
 #CC = gcc -O3 -DCAVEMAN_VERSION='"$(CAVEMAN_VERSION)"' -g
@@ -13,6 +12,12 @@ CC+= -O3 -g -DCAVEMAN_VERSION='"$(CAVEMAN_VERSION)"' -DTEST_REF='"$(TEST_REF)"'
 # -Wall turns on most warnings from compiler
 CFLAGS = -Wall
 
+ifneq ($(DEBUG),)
+    CFLAGS += -O3  # Optimise
+else
+    CFLAGS += -g -O0  # Debug
+endif
+
 HTSLOC?=$(HTSLIB)
 
 HTSTMP?=./caveman_tmp
@@ -73,8 +78,14 @@ all: clean make_bin make_htslib_tmp $(CAVEMAN_TARGET) $(UMNORM_TARGET) copyscrip
 $(UMNORM_TARGET): $(OBJS)
 	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(UMNORM_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/generateCavemanVCFUnmatchedNormalPanel.c
 
+ifneq ($(DEBUG),)
+$(CAVEMAN_TARGET): $(OBJS)
+	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(CAVEMAN_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/caveman.c
+else
 $(CAVEMAN_TARGET): $(OBJS)
 	$(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(CAVEMAN_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/caveman.c
+	strip $(CAVEMAN_TARGET)
+endif
 
 #Unit Tests
 test: $(CAVEMAN_TARGET)

setup.sh

@@ -32,12 +32,19 @@ function version_eq_gt() {
 
 set -euo pipefail 
 
-if [ "$#" -ne "1" ] ; then
+if [ "$#" -lt "1" ] ; then
   echo "Please provide an installation path  such as /opt/pancan"
   exit 0
 fi
 
 INST_PATH=$1
+DEBUG_ARG="${2:-}"
+if [ "$DEBUG_ARG" = "DEBUG" ]; then
+  DEBUG_FLAG=1
+  echo "DEBUG set"
+else
+  DEBUG_FLAG=0
+fi
 
 CPU=`grep -c ^processor /proc/cpuinfo`
 if [ $? -eq 0 ]; then
@@ -52,9 +59,9 @@ echo "Max compilation CPUs set to $CPU"
 # get current directory
 INIT_DIR=`pwd`
 
-set +o pipefail
-LIBZ_VER=$(echo '#include <zlib.h>' | cpp -H -o /dev/null |& head -1 | cut -d' ' -f 2 | xargs grep -e '#define ZLIB_VERSION' | cut -d ' ' -f 3 | perl -pe 's/["\n]//g')
-set -o pipefail
+echo '#include <zlib.h>' | cpp -H 1>/dev/null 2> tmp.log.cpp
+LIBZ_VER=$(cat tmp.log.cpp | head -1 | cut -d' ' -f 2 | xargs grep -e '#define ZLIB_VERSION' | cut -d ' ' -f 3 | sed 's/"//g')
+rm tmp.log.cpp
 
 if version_eq_gt $LIBZ_VER $REQUIRED_MIN_LIBZ ; then
 	echo "Found acceptable libz version $LIBZ_VER."
@@ -111,23 +118,35 @@ export HTSLIB="$SETUP_DIR/htslib"
 export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${HTSLIB}:${LINASM_LIB}"
 
 echo -n "Building CaVEMan ..."
-if [ -e "$SETUP_DIR/caveman.success" ]; then
-  echo -n " previously installed ...";
+cd $INIT_DIR
+make clean &&
+{
+if [ $DEBUG_FLAG -eq 1 ]; then
+  make -j$CPU DEBUG=1
 else
-  cd $INIT_DIR
-  make clean &&
-  make -j$CPU &&
-  mv $INIT_DIR/bin/* $INST_PATH/bin/ &&
-  mkdir -p $INST_PATH/lib/ &&
-  cp $LINASM_LIB/liblinasm.so $INST_PATH/lib/. &&
-  touch $SETUP_DIR/caveman.success
+  make -j$CPU
 fi
+} &&
+mv $INIT_DIR/bin/* $INST_PATH/bin/ &&
+mkdir -p $INST_PATH/lib/ &&
+cp $LINASM_LIB/liblinasm.so $INST_PATH/lib/. &&
+touch $SETUP_DIR/caveman.success
 
-# cleanup all junk
-rm -rf $SETUP_DIR 
-make clean
+# cleanup all intermediates
+if [ -e "$SETUP_DIR/caveman.success" ]; then
+  echo
+  echo "Installation succesful"
+  echo "Binaries available at $INST_PATH/bin/"
+  echo "linasm.so available at $INST_PATH/lib/ - directory must be on LD_LIBRARY_PATH"
+  if [ $DEBUG_FLAG -eq 1 ]; then
+    echo "DEBUG set, retaining intermediate files"
+  else
+    rm -rf $SETUP_DIR
+    make clean
+  fi
+else
+  echo
+  echo "Installation failed"
+  echo "Retaining intermediate files"
+fi
 
-echo
-echo "Installation succesful"
-echo "Binaries available at $INST_PATH/bin/"
-echo "linasm.so available at $INST_PATH/lib/ - directory must be on LD_LIBRARY_PATH"

src/alg_bean.h

@@ -34,7 +34,7 @@
 #define _alg_bean_h
 
 #include <stdio.h>
-#include <List.h>
+#include "List.h"
 #include "khash.h"
 
 //New hash to store unique readlengths

src/caveman.c

@@ -30,12 +30,12 @@
 *
 */
 
-#include <setup.h>
-#include <split.h>
-#include <mstep.h>
-#include <merge.h>
-#include <estep.h>
-#include <dbg.h>
+#include "setup.h"
+#include "split.h"
+#include "mstep.h"
+#include "merge.h"
+#include "estep.h"
+#include "dbg.h"
 #include <stdio.h>
 #include <stdlib.h>
 #include <getopt.h>

src/fai_access.c

@@ -35,7 +35,7 @@
 #include <string.h>
 #include <stdlib.h>
 #include "dbg.h"
-#include <fai_access.h>
+#include "fai_access.h"
 
 int fai_access_get_name_from_index(int idx, char *index_file_name, char *chr_name, int *length){
 	assert(index_file_name != NULL);

src/ignore_reg_access.c

@@ -36,8 +36,8 @@
 #include "dbg.h"
 #include <string.h>
 #include <limits.h>
-#include <alg_bean.h>
-#include <ignore_reg_access.h>
+#include "alg_bean.h"
+#include "ignore_reg_access.h"
 
 int ignore_reg_access_get_ign_reg_count_for_chr(char *ign_file, char *chr){
      assert(ign_file != NULL);
@@ -111,7 +111,7 @@ int ignore_reg_access_get_ign_reg_for_chr(char *ign_file,char *chr, int entry_co
         int chk = sscanf(rd,"%s\t%d\t%d",chr_nom,&beg,&end);
         if(chk==3){
             if(strcmp(chr_nom,chr) == 0){
-                regions[found_count] = malloc(sizeof(struct seq_region_t));
+                regions[found_count] = malloc(sizeof(struct seq_region_t));  // not free'd :/
                 check_mem(regions[found_count]);
                 regions[found_count]->beg = beg + is_bed;
                 regions[found_count]->end = end;

src/ignore_reg_access.h

@@ -34,7 +34,7 @@
 #define _ignore_reg_access_h
 
 #include <stdio.h>
-#include <List.h>
+#include "List.h"
 
 typedef struct seq_region_t{
    int beg;

src/split.c

@@ -35,11 +35,11 @@
 #include <getopt.h>
 #include <string.h>
 #include <assert.h>
-#include <dbg.h>
-#include <split.h>
-#include <file_tests.h>
-#include <alg_bean.h>
-#include <fai_access.h>
+#include "dbg.h"
+#include "split.h"
+#include "file_tests.h"
+#include "alg_bean.h"
+#include "fai_access.h"
 #include <split_access.h>
 #include <bam_access.h>
 #include <config_file_access.h>
@@ -179,7 +179,7 @@ int split_main(int argc, char *argv[]){
     int is_err = split_setup_options(argc,argv);
     check(is_err==0,"Error parsing options");
 
-    char *chr_name = malloc(sizeof(char *));
+    char *chr_name = malloc(sizeof(char) * 100);
     //Open the config file and do relevant things
     FILE *config = fopen(config_file,"r");
     check(config != NULL,"Failed to open config file for reading. Have you run caveman-setup?");
@@ -428,6 +428,8 @@ int split_main(int argc, char *argv[]){
         hts_itr_destroy(iter_tum);
     }//End of checking if this is a valid contig to split.
 
+    free(ignore_regs);
+    free(chr_name);
 
     return 0;
 error:

src/split.h

@@ -33,8 +33,8 @@
 #ifndef _split_h
 #define _split_h
 
-#include <List.h>
-#include <ignore_reg_access.h>
+#include "List.h"
+#include "ignore_reg_access.h"
 
 int get_read_counts_with_ignore(List *ignore,int start, int stop, char *chr);
 int shrink_section_to_size(char *chr_name,int sect_start, int sect_stop,