removed unnecessary fasta_file.h

bwa-mem2 · Aug 2, 2019 · 97a2db0 · 97a2db0
1 parent a9fd42d
commit 97a2db0
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Showing 5 changed files with 18 additions and 194 deletions.
diff --git a/Makefile b/Makefile
@@ -117,7 +117,6 @@ src/fastmap.o: src/fastmap.h src/bwa.h src/bntseq.h src/bwt.h src/macro.h
 src/fastmap.o: src/bwamem.h src/kthread.h src/bandedSWA.h src/kstring.h
 src/fastmap.o: src/ksw.h src/kvec.h src/ksort.h src/utils.h src/profiling.h
 src/fastmap.o: src/FMI_search.h src/read_index_ele.h src/kseq.h
-src/fastmap.o: src/fasta_file.h
 src/kstring.o: src/kstring.h
 src/ksw.o: src/ksw.h src/macro.h
 src/kswv.o: src/kswv.h src/macro.h src/ksw.h src/bandedSWA.h

diff --git a/src/bntseq.cpp b/src/bntseq.cpp
@@ -236,6 +236,7 @@ void bns_destroy(bntseq_t *bns)
 
 static uint8_t *add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_pac, int *m_seqs, int *m_holes, bntamb1_t **q)
 {
+	fprintf(stderr, "%s\n", seq->name);
 	bntann1_t *p;
 	int i, lasts;
 	if (bns->n_seqs == *m_seqs) {

diff --git a/src/fasta_file.h b/src/fasta_file.h
diff --git a/src/fastmap.cpp b/src/fastmap.cpp
@@ -41,7 +41,7 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
 #include <sstream>
 #include "fastmap.h"
 #include "FMI_search.h"
-#include "fasta_file.h"
+// #include "fasta_file.h"
 #if 0 && (__linux__)
 #include <sys/sysinfo.h>
 #endif

diff --git a/src/profiling.cpp b/src/profiling.cpp
@@ -165,6 +165,22 @@ int display_stats()
 	fprintf(stderr, "\n\tTotal allocs: %d = %d out total requests: %d, Rate: %0.2f\n",
 			agg1, agg3, agg2, agg1*1.0/agg2);
 
+#if HIDE
+	fprintf(stderr, "\n BSW Perf.:\n");
+	find_opt(tprof[MEM_ALN2_B], 1, &max, &min, &avg);
+	fprintf(stderr, "\tLeft 16-bit time avg: %0.2lf, (%0.2lf, %0.2lf)\n",
+			avg*1.0/proc_freq, max*1.0/proc_freq, min*1.0/proc_freq);
+	find_opt(tprof[MEM_ALN2_D], 1, &max, &min, &avg);
+	fprintf(stderr, "\tLeft 8-bit time avg: %0.2lf, (%0.2lf, %0.2lf)\n",
+			avg*1.0/proc_freq, max*1.0/proc_freq, min*1.0/proc_freq);
+	find_opt(tprof[MEM_ALN2_C], 1, &max, &min, &avg);
+	fprintf(stderr, "\tRight 16-bit time avg: %0.2lf, (%0.2lf, %0.2lf)\n",
+			avg*1.0/proc_freq, max*1.0/proc_freq, min*1.0/proc_freq);
+	find_opt(tprof[MEM_ALN2_E], 1, &max, &min, &avg);
+	fprintf(stderr, "\tRight 8-bit time avg: %0.2lf, (%0.2lf, %0.2lf)\n",
+			avg*1.0/proc_freq, max*1.0/proc_freq, min*1.0/proc_freq);
+#endif
+
 #if HIDE
 	fprintf(stderr, "\nSTATSV\n");
 	fprintf(stderr, "%0.2lf\n",	tprof[PROCESS][0]*1.0/proc_freq);