SplitReadAll_lite.c: "samtoolsexec" was missing as argument in some sprintf statements.
"samtoolsexec" was missing as argument in some sprintf statements.
This solves those compiling warnings (and 2 actual bugs):
SplitReadAll_lite.c: In function ‘main’:
SplitReadAll_lite.c:146:3: warning: too few arguments for format
SplitReadAll_lite.c:304:3: warning: too few arguments for format
--- a/SplitReadAll_lite.c
+++ b/SplitReadAll_lite.c
@@ -143,7 +143,7 @@ int main(int argc, char** argv) {
fflush(stdout);
//res = system(cmd);
- sprintf(cmd,"%s sort %s.inv.evert.bam %s.inv.evert.sorted\n",outdir,outdir);
+ sprintf(cmd,"%s sort %s.inv.evert.bam %s.inv.evert.sorted\n",samtoolsexec,outdir,outdir);
printf("%s\n",cmd);
fflush(stdout);
//res = system(cmd);
@@ -301,7 +301,7 @@ int main(int argc, char** argv) {
//Transform the outdir.single.txt to bam and remove intermediate files
- sprintf(cmd,"%s view -bt %s %s.single.txt > %s.single.bam\n",refindex,outdir,outdir);
+ sprintf(cmd,"%s view -bt %s %s.single.txt > %s.single.bam\n",samtoolsexec,refindex,outdir,outdir);
printf("%s\n",cmd);
fflush(stdout);
//res = system(cmd);
