Merge pull request #4 from dpryan79/fix3

Fix #3
dpryan79 · Dec 30, 2015 · a4c7f18 · a4c7f18
2 parents a80436a + e489f8d
commit a4c7f18
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Showing 8 changed files with 43 additions and 35 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,10 @@
+sudo: false
+language: c
+os:
+  - linux
+  - osx
+env: MPI=openmpi
+script: make
+compiler:
+  - clang
+  - gcc
diff --git a/Makefile b/Makefile
@@ -1,8 +1,8 @@
 #Please see the tutorial (http://sourceforge.net/projects/dna-bison/files/bison_tutorial.tar.gz/download) for help in setting these options.
-WORK=/home/ryand#This should be changed to match your needs
-PREFIX = $(WORK)/bin
-CC = mpicc
-HTSLIB=htslib/libhts.a #Use -lhtslib and set LIB_DIRS for dynamic linkage
+WORK?=/home/ryand#This should be changed to match your needs
+PREFIX ?= $(WORK)/bin
+CC ?= mpicc
+HTSLIB ?= htslib/libhts.a #Use -lhtslib and set LIB_DIRS for dynamic linkage
 INCLUDE_DIRS = -Ihtslib
 LIB_DIRS =
 OPTS = -Wall -g #-DDEBUG #-DNOTHROTTLE

diff --git a/herd/main.c b/herd/main.c
@@ -150,17 +150,6 @@ int main(int argc, char *argv[]) {
     char processor_name[MPI_MAX_PROCESSOR_NAME];
 #endif
 
-    //Deal with MPI initialization, this seems like an odd way to do things.
-    MPI_Init_thread(NULL, NULL, MPI_THREAD_MULTIPLE, &provided);
-    if(provided != MPI_THREAD_MULTIPLE) {
-        fprintf(stderr, "You're MPI implementation doesn't support MPI_THREAD_MULTIPLE, which is required for bison_herd to work.\n");
-        return -1;
-    }
-#ifndef DEBUG
-    MPI_Comm_rank(MPI_COMM_WORLD, &taskid);
-    MPI_Get_processor_name(processor_name, &name_len);
-#endif
-
     config.odir = NULL;
     config.paired = 0; //Default is single-ended
     config.directional = 0; //Default is non-directional
@@ -330,6 +319,16 @@ int main(int argc, char *argv[]) {
         }
     }
 
+    MPI_Init_thread(NULL, NULL, MPI_THREAD_MULTIPLE, &provided);
+    if(provided != MPI_THREAD_MULTIPLE) {
+        fprintf(stderr, "You're MPI implementation doesn't support MPI_THREAD_MULTIPLE, which is required for bison_herd to work.\n");
+        return -1;
+    }
+#ifndef DEBUG
+    MPI_Comm_rank(MPI_COMM_WORLD, &taskid);
+    MPI_Get_processor_name(processor_name, &name_len);
+#endif
+
     if(config.FASTQ1 == NULL || config.genome_dir == NULL || (config.FASTQ2 == NULL && config.paired == 1)) {
         if(taskid == MASTER) {
             fprintf(stderr, "No FASTQ files!\n");

diff --git a/htslib b/htslib
diff --git a/main.c b/main.c
@@ -102,19 +102,6 @@ int main(int argc, char *argv[]) {
     char processor_name[MPI_MAX_PROCESSOR_NAME];
 #endif
 
-    //Deal with MPI initialization, this seems like an odd way to do things.
-#ifndef DEBUG
-    MPI_Init_thread(NULL, NULL, MPI_THREAD_FUNNELED, &provided);
-    MPI_Comm_rank(MPI_COMM_WORLD, &taskid);
-    MPI_Get_processor_name(processor_name, &name_len);
-#else
-    MPI_Init_thread(NULL, NULL, MPI_THREAD_FUNNELED, &provided);
-#endif
-    if(provided != MPI_THREAD_FUNNELED) {
-        fprintf(stderr, "Your implementation does not support MPI_THREAD_FUNNELED, which is required for bison to run. This is actually quite unusual!\n");
-        return -1;
-    }
-
     config.odir = NULL;
     config.paired = 0; //Default is single-ended
     config.directional = 0; //Default is non-directional
@@ -250,6 +237,18 @@ int main(int argc, char *argv[]) {
         }
     }
 
+#ifndef DEBUG
+    MPI_Init_thread(NULL, NULL, MPI_THREAD_FUNNELED, &provided);
+    MPI_Comm_rank(MPI_COMM_WORLD, &taskid);
+    MPI_Get_processor_name(processor_name, &name_len);
+#else
+    MPI_Init_thread(NULL, NULL, MPI_THREAD_FUNNELED, &provided);
+#endif
+    if(provided != MPI_THREAD_FUNNELED) {
+        fprintf(stderr, "Your implementation does not support MPI_THREAD_FUNNELED, which is required for bison to run. This is actually quite unusual!\n");
+        return -1;
+    }
+
 #ifndef DEBUG
     if(!config.quiet) {printf("%s has rank %i\n", processor_name, taskid); fflush(stderr);}
 #endif

diff --git a/markduplicates.c b/markduplicates.c
@@ -40,7 +40,7 @@ typedef struct {
 } qsort_func_struct;
 
 //Get the total phred score
-inline int32_t total_phred(bam1_t *read) {
+int32_t total_phred(bam1_t *read) {
     int32_t l = read->core.l_qseq;
     int32_t i=0, total=0;
     uint8_t *qual = bam_get_qual(read);
@@ -271,7 +271,7 @@ are on different chromosomes or different strand.\n");
            it's full). The default is 1000000.\n");
 }
 
-inline int32_t get_strand(bam1_t *read) {
+int32_t get_strand(bam1_t *read) {
     char *XG = bam_aux2Z(bam_aux_get(read, "XG"));
     char *XR = bam_aux2Z(bam_aux_get(read, "XR"));
 
@@ -294,7 +294,7 @@ inline int32_t get_strand(bam1_t *read) {
     }
 }
 
-inline int32_t get_pos(bam1_t *read) {
+int32_t get_pos(bam1_t *read) {
     int32_t pos = read->core.pos;
     uint32_t *CIGAR = bam_get_cigar(read);
     int32_t op, nops;
@@ -315,7 +315,7 @@ inline int32_t get_pos(bam1_t *read) {
 }
 
 //return the tid, such that first 2 bits denote the strand
-inline int32_t get_tid(bam1_t *read) {
+int32_t get_tid(bam1_t *read) {
     int32_t strand = get_strand(read);
 
     strand = strand << 30;

diff --git a/master.c b/master.c
@@ -76,7 +76,7 @@ int get_AS(bam1_t *read) {
 *   int32_t rlen: a read length
 *
 *******************************************************************************/
-inline int scoreMin(int32_t rlen) {
+int scoreMin(int32_t rlen) {
     //Return different values, depending on --score-min
     if(config.scoremin_type == 'L') {
         return (config.scoremin_intercept + config.scoremin_coef * rlen);

diff --git a/slurp.c b/slurp.c
@@ -34,7 +34,7 @@ void add_element(struct packed_struct *last, void *packed) {
 *   struct packed_struct *remove: element to destroy
 *
 *******************************************************************************/
-inline void destroy_element(struct packed_struct *remove) {
+void destroy_element(struct packed_struct *remove) {
     bam1_t *pbam1_t = remove->packed;
     if(pbam1_t != NULL) {
         if(pbam1_t->data != NULL) free(pbam1_t->data);
+0 −7		.gitignore
+17 −71		INSTALL
+18 −35		Makefile
+0 −50		NEWS
+0 −16		README.md
+2 −3		bgzf.c
+3 −0		config.h
+0 −72		config.mk.in
+0 −93		configure.ac
+24 −80		cram/cram_decode.c
+21 −74		cram/cram_encode.c
+23 −61		cram/cram_io.c
+17 −18		faidx.c
+1 −16		hfile.c
+1 −2		hfile_internal.h
+0 −243		hfile_irods.c
+18 −153		hts.c
+0 −71		htsfile.1
+3 −13		htsfile.c
+1 −2		htslib.mk
+2 −4		htslib/faidx.h
+1 −9		htslib/hfile.h
+2 −21		htslib/hts.h
+2 −10		htslib/hts_defs.h
+2 −9		htslib/regidx.h
+4 −4		htslib/vcf.h
+0 −8		htslib/vcf_sweep.h
+0 −8		htslib/vcfutils.h
+1 −1		tabix.1
+27 −2		tabix.c
+2 −19		test/sam.c
+1 −1		test/test_view.c