aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--src/indexamajig.c10
1 files changed, 8 insertions, 2 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c
index a89ecc5e..57d599b5 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -145,6 +145,8 @@ static void show_help(const char *s)
" --integrate-found Skip the spot prediction step, and just integrate\n"
" the intensities of the spots found by the initial\n"
" peak search.\n"
+" --no-peaks-in-stream Do not record peak search results in the stream.\n"
+" --no-refls-in-stream Do not record integrated reflections in the stream.\n"
);
}
@@ -199,6 +201,8 @@ int main(int argc, char *argv[])
int use_saturated = 0;
int no_revalidate = 0;
int integrate_found = 0;
+ int config_nopeaks = 0;
+ int config_norefls = 0;
/* For ease of upgrading from old method */
char *scellr = NULL;
@@ -249,6 +253,8 @@ int main(int argc, char *argv[])
{"min-integration-snr",1, NULL, 12},
{"tolerance", 1, NULL, 13},
{"int-radius", 1, NULL, 14},
+ {"no-peaks-in-stream", 1, &config_nopeaks, 1},
+ {"no-refls-in-stream", 1, &config_norefls, 1},
/* FIXME: Add '--no-peaks' and '--no-reflections' */
@@ -574,8 +580,8 @@ int main(int argc, char *argv[])
iargs.integrate_saturated = integrate_saturated;
iargs.no_revalidate = no_revalidate;
iargs.integrate_found = integrate_found;
- iargs.include_peaks = 1;
- iargs.include_reflections = 1; /* FIXME! */
+ iargs.include_peaks = !config_nopeaks;
+ iargs.include_reflections = !config_norefls;
create_sandbox(&iargs, n_proc, prefix, config_basename, fh,
use_this_one_instead, ofh, argc, argv);