biology/bio-mocha: Update to 1.14-20220112

Upstream incorporated my patches to eliminate nested functions, which
are not standard C and pose security risks.
A few other minor updated.

5 files changed, 8 insertions, 507 deletions

diff --git a/biology/bio-mocha/Makefile b/biology/bio-mocha/Makefile
index ec134d0530bb..f7191a9f286b 100644
--- a/biology/bio-mocha/Makefile
+++ b/biology/bio-mocha/Makefile
@@ -1,9 +1,8 @@
 PORTNAME=	bio-mocha
-DISTVERSION=	1.13
-PORTREVISION=	1
+DISTVERSION=	1.14
 CATEGORIES=	biology
 MASTER_SITES=	https://software.broadinstitute.org/software/mocha/
-DISTFILES+=	${PORTNAME}_${DISTVERSION}-20211015.tar.gz
+DISTFILES+=	${PORTNAME}_${DISTVERSION}-20220112.tar.gz
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Bcftools plugin for mosaic chromosomal alteration analysis
diff --git a/biology/bio-mocha/distinfo b/biology/bio-mocha/distinfo
index ee4554ecbe66..392157da945c 100644
--- a/biology/bio-mocha/distinfo
+++ b/biology/bio-mocha/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1640100283
-SHA256 (bio-mocha_1.13-20211015.tar.gz) = e145bb48fea347202e16395ab7d78e7e7314749b8d472a2071f8074004cd63a5
-SIZE (bio-mocha_1.13-20211015.tar.gz) = 73627
-SHA256 (samtools-bcftools-1.13-1.14_GH0.tar.gz) = c9a814b1f0a13af19b45283f039d01b524e011d870ac95cd92e6907c3d1db6d1
-SIZE (samtools-bcftools-1.13-1.14_GH0.tar.gz) = 3326994
+TIMESTAMP = 1642078792
+SHA256 (bio-mocha_1.14-20220112.tar.gz) = 189a522418f12cbb04e6c5ccae130dbae1682907808f4cb594af4ff386651068
+SIZE (bio-mocha_1.14-20220112.tar.gz) = 75910
+SHA256 (samtools-bcftools-1.14_GH0.tar.gz) = c9a814b1f0a13af19b45283f039d01b524e011d870ac95cd92e6907c3d1db6d1
+SIZE (samtools-bcftools-1.14_GH0.tar.gz) = 3326994
diff --git a/biology/bio-mocha/files/patch-plugins_beta__binom.h b/biology/bio-mocha/files/patch-plugins_beta__binom.h
deleted file mode 100644
index a6804a6dc9f4..000000000000
--- a/biology/bio-mocha/files/patch-plugins_beta__binom.h
+++ /dev/null
@@ -1,19 +0,0 @@
---- plugins/beta_binom.h.orig	2021-11-30 13:41:36 UTC
-+++ plugins/beta_binom.h
-@@ -137,14 +137,14 @@ void beta_binom_update(beta_binom_t *self, double p, d
-  *  Returns the equivalent of dbeta_binom(a, a+b, p, (1 - rho) / rho, log=TRUE) from R package
-  * rmutil
-  */
--inline double beta_binom_log_unsafe(const beta_binom_t *self, int a, int b) {
-+static inline double beta_binom_log_unsafe(const beta_binom_t *self, int a, int b) {
-     return self->log_gamma_alpha[a] + self->log_gamma_beta[b] - self->log_gamma_alpha_beta[a + b];
- }
- 
- /**
-  *  Same as before but it performs boundary checking before computing the log likelihood
-  */
--inline double beta_binom_log(beta_binom_t *self, int a, int b) {
-+static inline double beta_binom_log(beta_binom_t *self, int a, int b) {
-     if (a < 0 || b < 0) return NAN;
-     if (a > self->n1 || b > self->n1 || a + b > self->n2)
-         beta_binom_update(self, self->p, self->rho, a > b ? a : b, a + b);
diff --git a/biology/bio-mocha/files/patch-plugins_mocha.c b/biology/bio-mocha/files/patch-plugins_mocha.c
deleted file mode 100644
index 665d785c00f3..000000000000
--- a/biology/bio-mocha/files/patch-plugins_mocha.c
+++ /dev/null
@@ -1,479 +0,0 @@
---- plugins/mocha.c.orig	2021-10-15 02:37:57 UTC
-+++ plugins/mocha.c
-@@ -705,6 +705,44 @@ static double baf_phase_lod(const float *baf_arr, cons
-     return (double)ret * M_LOG10E;
- }
- 
-+typedef struct
-+{
-+    const float *baf;
-+    const int8_t *gt_phase;
-+    int n;
-+    const int *imap;
-+    int8_t *path;
-+    float err_log_prb;
-+    float baf_sd;
-+}   f1_data_t;
-+
-+double f1(double x, void *data)
-+{
-+    f1_data_t	*d = data;
-+
-+    return -baf_phase_lod(d->baf, d->gt_phase, d->n, d->imap, d->path,
-+                          d->err_log_prb, d->baf_sd, x);
-+}
-+
-+static inline f1_data_t *f1_pack(const float *baf, const int8_t *gt_phase, int n,
-+		   const int *imap, int8_t *path, float err_log_prb,
-+		   float baf_sd)
-+{
-+    // Switch to malloc() and free() if more than one object must exist at
-+    // any given time
-+    f1_data_t	*d = malloc(sizeof(f1_data_t));
-+
-+    d->baf = baf;
-+    d->gt_phase = gt_phase;
-+    d->n = n;
-+    d->imap = imap;
-+    d->path = path;
-+    d->err_log_prb = err_log_prb;
-+    d->baf_sd = baf_sd;
-+
-+    return d;
-+}
-+
- // TODO find a better title for this function
- static float compare_models(const float *baf, const int8_t *gt_phase, int n, const int *imap, float xy_log_prb,
-                             float err_log_prb, float flip_log_prb, float tel_log_prb, float baf_sd, const float *bdev,
-@@ -716,8 +754,11 @@ static float compare_models(const float *baf, const in
-     int n_flips = 0;
-     for (int i = 1; i < n; i++)
-         if (path[i - 1] && path[i] && path[i - 1] != path[i]) n_flips++;
--    double f(double x, void *data) { return -baf_phase_lod(baf, gt_phase, n, imap, path, err_log_prb, baf_sd, x); }
--    double x, fx = kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &x);
-+    double x;
-+    f1_data_t *f1_data = f1_pack(baf, gt_phase, n, imap, path, err_log_prb,
-+				 baf_sd);
-+    double fx = kmin_brent(f1, 0.1, 0.2, f1_data, KMIN_EPS, &x);
-+    free(f1_data);
-     free(path);
-     return -(float)fx + (float)n_flips * flip_log_prb * (float)M_LOG10E;
- }
-@@ -750,6 +791,34 @@ static float get_sample_mean(const float *v, int n, co
-     return mean /= (float)j;
- }
- 
-+typedef struct
-+{
-+    const float *baf_arr;
-+    int n;
-+    const int *imap;
-+    float baf_sd;
-+}   f7_data_t;
-+
-+double f7(double x, void *data)
-+{
-+    f7_data_t *d = data;
-+
-+    return -baf_log_lkl(d->baf_arr, d->n, d->imap, d->baf_sd, x);
-+}
-+
-+static inline f7_data_t *f7_pack(const float *baf_arr, int n, const int *imap,
-+    float baf_sd)
-+{
-+    f7_data_t *d = malloc(sizeof(f7_data_t));
-+
-+    d->baf_arr = baf_arr;
-+    d->n = n;
-+    d->imap = imap;
-+    d->baf_sd = baf_sd;
-+
-+    return d;
-+}
-+
- static float get_baf_bdev(const float *baf_arr, int n, const int *imap, float baf_sd) {
-     double bdev = 0.0;
-     int j = 0;
-@@ -763,8 +832,9 @@ static float get_baf_bdev(const float *baf_arr, int n,
-     bdev /= j;
-     // simple method to compute bdev should work well for germline duplications
-     if ((float)bdev > 2.0f * baf_sd) return (float)bdev;
--    double f(double x, void *data) { return -baf_log_lkl(baf_arr, n, imap, baf_sd, x); }
--    kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &bdev);
-+    f7_data_t *f7_data = f7_pack(baf_arr, n, imap, baf_sd);
-+    kmin_brent(f7, 0.1, 0.2, f7_data, KMIN_EPS, &bdev);
-+    free(f7_data);
-     return (float)bdev < 1e-4 ? (float)NAN : (float)bdev;
- }
- 
-@@ -801,10 +871,41 @@ static double ad_log_lkl(const int16_t *ad0_arr, const
-     return (double)ret * M_LOG10E;
- }
- 
-+typedef struct
-+{
-+    const int16_t *ad0_arr;
-+    const int16_t *ad1_arr;
-+    int n;
-+    const int *imap;
-+    float ad_rho;
-+}   f5_data_t;
-+
-+double f5(double x, void *data)
-+{
-+    f5_data_t *d = data;
-+
-+    return -ad_log_lkl(d->ad0_arr, d->ad1_arr, d->n, d->imap, d->ad_rho, x);
-+}
-+
-+static inline f5_data_t *f5_pack(const int16_t *ad0_arr,
-+    const int16_t *ad1_arr, int n, const int *imap, float ad_rho)
-+{
-+    f5_data_t *d = malloc(sizeof(f5_data_t));
-+
-+    d->ad0_arr = ad0_arr;
-+    d->ad1_arr = ad1_arr;
-+    d->n = n;
-+    d->imap = imap;
-+    d->ad_rho = ad_rho;
-+
-+    return d;
-+}
-+
- static float get_ad_bdev(const int16_t *ad0_arr, const int16_t *ad1_arr, int n, const int *imap, float ad_rho) {
-     double bdev = 0.0;
--    double f(double x, void *data) { return -ad_log_lkl(ad0_arr, ad1_arr, n, imap, ad_rho, x); }
--    kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &bdev);
-+    f5_data_t *f5_data = f5_pack(ad0_arr, ad1_arr, n, imap, ad_rho);
-+    kmin_brent(f5, 0.1, 0.2, f5_data, KMIN_EPS, &bdev);
-+    free(f5_data);
-     return (float)bdev < 1e-4 ? (float)NAN : (float)bdev;
- }
- 
-@@ -986,6 +1087,44 @@ static double ad_phase_lod(const int16_t *ad0_arr, con
-     return (double)ret * M_LOG10E;
- }
- 
-+typedef struct
-+{
-+    const int16_t *ad0;
-+    const int16_t *ad1;
-+    const int8_t *gt_phase;
-+    int n;
-+    const int *imap;
-+    int8_t *path;
-+    float err_log_prb;
-+    float ad_rho;
-+}   f4_data_t;
-+
-+double f4(double x, void *data)
-+{
-+    f4_data_t *d = data;
-+
-+    return -ad_phase_lod(d->ad0, d->ad1, d->gt_phase, d->n, d->imap, d->path,
-+        d->err_log_prb, d->ad_rho, x);
-+}
-+
-+static inline f4_data_t *f4_pack(const int16_t *ad0, const int16_t *ad1,
-+    const int8_t *gt_phase, int n, const int *imap, int8_t *path,
-+    float err_log_prb, float ad_rho)
-+{
-+    f4_data_t *d = malloc(sizeof(f4_data_t));
-+
-+    d->ad0 = ad0;
-+    d->ad1 = ad1;
-+    d->gt_phase = gt_phase;
-+    d->n = n;
-+    d->imap = imap;
-+    d->path = path;
-+    d->err_log_prb = err_log_prb;
-+    d->ad_rho = ad_rho;
-+
-+    return d;
-+}
-+
- // TODO find a better title for this function
- static float compare_wgs_models(const int16_t *ad0, const int16_t *ad1, const int8_t *gt_phase, int n, const int *imap,
-                                 float xy_log_prb, float err_log_prb, float flip_log_prb, float tel_log_prb,
-@@ -998,8 +1137,9 @@ static float compare_wgs_models(const int16_t *ad0, co
-     int n_flips = 0;
-     for (int i = 1; i < n; i++)
-         if (path[i - 1] && path[i] && path[i - 1] != path[i]) n_flips++;
--    double f(double x, void *data) { return -ad_phase_lod(ad0, ad1, gt_phase, n, imap, path, err_log_prb, ad_rho, x); }
--    double x, fx = kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &x);
-+    f4_data_t *f4_data = f4_pack(ad0, ad1, gt_phase, n, imap, path, err_log_prb, ad_rho);
-+    double x, fx = kmin_brent(f4, 0.1, 0.2, f4_data, KMIN_EPS, &x);
-+    free(f4_data);
-     free(path);
-     return -(float)fx + (float)n_flips * flip_log_prb * (float)M_LOG10E;
- }
-@@ -1485,6 +1625,129 @@ static float get_path_segs(const int8_t *path, const f
-     return 0;
- }
- 
-+typedef struct
-+{
-+    float *lrr;
-+    int a;
-+    int16_t *ad0;
-+    int16_t *ad1;
-+    mocha_t *mocha;
-+    const model_t *model;
-+    sample_t *self;
-+    float *baf;
-+}   f3_data_t;
-+    
-+double f3(double x, void *data)
-+{
-+    f3_data_t *d = data;
-+
-+    if (d->model->flags & WGS_DATA)
-+        return -lrr_ad_lod(d->lrr + d->a, d->ad0 + d->a, d->ad1 + d->a,
-+            d->mocha->n_sites, NULL, NAN, d->model->lrr_bias,
-+            d->model->lrr_hap2dip, d->self->adjlrr_sd,
-+            d->self->stats.dispersion, x);
-+    else
-+        return -lrr_baf_lod(d->lrr + d->a, d->baf + d->a, d->mocha->n_sites,
-+            NULL, NAN, d->model->lrr_bias, d->model->lrr_hap2dip,
-+            d->self->adjlrr_sd, d->self->stats.dispersion, x);
-+}
-+
-+static inline f3_data_t *f3_pack(float *lrr, int a, int16_t *ad0, int16_t *ad1,
-+    mocha_t *mocha, const model_t *model, sample_t *self, float *baf)
-+
-+{
-+    f3_data_t *d = malloc(sizeof(f3_data_t));
-+
-+    d->lrr = lrr;
-+    d->a = a;
-+    d->ad0 = ad0;
-+    d->ad1 = ad1;
-+    d->mocha = mocha;
-+    d->model = model;
-+    d->self = self;
-+    d->baf = baf;
-+
-+    return d;
-+}
-+
-+typedef struct
-+{
-+    int16_t *ad0;
-+    int16_t *ad1;
-+    int8_t *gt_phase;
-+    mocha_t *mocha;
-+    int *imap_arr;
-+    int *beg;
-+    int i;
-+    int8_t *path;
-+    sample_t *self;
-+}   f6_data_t;
-+
-+double f6(double x, void *data)
-+{
-+    f6_data_t *d = data;
-+
-+    return -ad_phase_lod(d->ad0, d->ad1, d->gt_phase, d->mocha->n_hets,
-+        d->imap_arr + d->beg[d->i], d->path + d->beg[d->i], NAN, d->self->stats.dispersion, x);
-+}
-+
-+static inline f6_data_t *f6_pack(int16_t *ad0, int16_t *ad1, int8_t *gt_phase,
-+    mocha_t *mocha, int *imap_arr, int *beg, int i, int8_t *path, sample_t *self)
-+
-+{
-+    f6_data_t *d = malloc(sizeof(f6_data_t));
-+
-+    d->ad0 = ad0;
-+    d->ad1 = ad1;
-+    d->gt_phase = gt_phase;
-+    d->mocha = mocha;
-+    d->imap_arr = imap_arr;
-+    d->beg = beg;
-+    d->i = i;
-+    d->path = path;
-+    d->self = self;
-+
-+    return d;
-+}
-+
-+typedef struct
-+{
-+    float *baf;
-+    int8_t *gt_phase;
-+    mocha_t *mocha;
-+    int *imap_arr;
-+    int *beg;
-+    int i;
-+    int8_t *path;
-+    sample_t *self;
-+}   f8_data_t;
-+
-+double f8(double x, void *data)
-+{
-+    f8_data_t *d = data;
-+
-+    return -baf_phase_lod(d->baf, d->gt_phase, d->mocha->n_hets,
-+	d->imap_arr + d->beg[d->i], d->path + d->beg[d->i], NAN,
-+	d->self->stats.dispersion, x);
-+}
-+
-+static inline f8_data_t *f8_pack(float *baf, int8_t *gt_phase, mocha_t *mocha,
-+    int *imap_arr, int *beg, int i, int8_t *path, sample_t *self)
-+{
-+    f8_data_t *d = malloc(sizeof(f8_data_t));
-+
-+    d->baf = baf;
-+    d->gt_phase = gt_phase;
-+    d->mocha = mocha;
-+    d->imap_arr = imap_arr;
-+    d->beg = beg;
-+    d->i = i;
-+    d->path = path;
-+    d->self = self;
-+
-+    return d;
-+}
-+
- // process one contig for one sample
- static void sample_run(sample_t *self, mocha_table_t *mocha_table, const model_t *model) {
-     // do nothing if chromosome Y or MT are being tested
-@@ -1735,16 +1998,11 @@ static void sample_run(sample_t *self, mocha_table_t *
-             mocha.ldev = get_median(lrr + a, b + 1 - a, NULL);
-             get_mocha_stats(pos, lrr, baf, gt_phase, n, a, b, cen_beg, cen_end, length, self->stats.baf_conc, &mocha);
- 
--            double f(double x, void *data) {
--                if (model->flags & WGS_DATA)
--                    return -lrr_ad_lod(lrr + a, ad0 + a, ad1 + a, mocha.n_sites, NULL, NAN, model->lrr_bias,
--                                       model->lrr_hap2dip, self->adjlrr_sd, self->stats.dispersion, x);
--                else
--                    return -lrr_baf_lod(lrr + a, baf + a, mocha.n_sites, NULL, NAN, model->lrr_bias, model->lrr_hap2dip,
--                                        self->adjlrr_sd, self->stats.dispersion, x);
--            }
-             double bdev_lrr_baf;
--            kmin_brent(f, -0.15, 0.15, NULL, KMIN_EPS, &bdev_lrr_baf);
-+            f3_data_t *f3_data = f3_pack(lrr, a, ad0, ad1, &mocha, model,
-+                 self, baf);
-+            kmin_brent(f3, -0.15, 0.15, f3_data, KMIN_EPS, &bdev_lrr_baf);
-+	    free(f3_data);
-             if (model->flags & WGS_DATA)
-                 mocha.lod_lrr_baf =
-                     lrr_ad_lod(lrr + a, ad0 + a, ad1 + a, mocha.n_sites, NULL, model->err_log_prb, model->lrr_bias,
-@@ -1796,23 +2054,21 @@ static void sample_run(sample_t *self, mocha_table_t *
-                     if (path[j] != path[j + 1]) mocha.n_flips++;
- 
-                 if (model->flags & WGS_DATA) {
--                    double f(double x, void *data) {
--                        return -ad_phase_lod(ad0, ad1, gt_phase, mocha.n_hets, imap_arr + beg[i], path + beg[i], NAN,
--                                             self->stats.dispersion, x);
--                    }
-                     double bdev;
--                    kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &bdev);
-+		    f6_data_t *f6_data = f6_pack(ad0, ad1, gt_phase, &mocha,
-+                        imap_arr, beg, i, path, self);
-+                    kmin_brent(f6, 0.1, 0.2, f6_data, KMIN_EPS, &bdev);
-+		    free(f6_data);
-                     mocha.bdev = fabsf((float)bdev);
-                     mocha.lod_baf_phase =
-                         ad_phase_lod(ad0, ad1, gt_phase, mocha.n_hets, imap_arr + beg[i], path + beg[i],
-                                      model->err_log_prb, self->stats.dispersion, mocha.bdev);
-                 } else {
--                    double f(double x, void *data) {
--                        return -baf_phase_lod(baf, gt_phase, mocha.n_hets, imap_arr + beg[i], path + beg[i], NAN,
--                                              self->stats.dispersion, x);
--                    }
-                     double bdev;
--                    kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &bdev);
-+		    f8_data_t *f8_data = f8_pack(baf, gt_phase, &mocha,
-+			imap_arr, beg, i, path, self);
-+                    kmin_brent(f8, 0.1, 0.2, f8_data, KMIN_EPS, &bdev);
-+		    free(f8_data);
-                     mocha.bdev = fabsf((float)bdev);
-                     mocha.lod_baf_phase = baf_phase_lod(baf, gt_phase, mocha.n_hets, imap_arr + beg[i], path + beg[i],
-                                                         model->err_log_prb, self->stats.dispersion, mocha.bdev);
-@@ -1923,6 +2179,60 @@ static float get_lrr_cutoff(const float *v, int n) {
-     return cutoff;
- }
- 
-+typedef struct
-+{
-+    int16_t *ad0;
-+    int16_t *ad1;
-+    int n;
-+}   f2_data_t;
-+
-+double f2(double x, void *data)
-+{
-+    f2_data_t *d = data;
-+
-+    return -lod_lkl_beta_binomial(d->ad0, d->ad1, d->n, NULL, x);
-+}
-+
-+static inline f2_data_t *f2_pack(int16_t *ad0, int16_t *ad1, int n)
-+
-+{
-+    f2_data_t *d = malloc(sizeof(f2_data_t));
-+
-+    d->ad0 = ad0;
-+    d->ad1 = ad1;
-+    d->n = n;
-+
-+    return d;
-+}
-+
-+typedef struct
-+{
-+    int16_t *ad0;
-+    int16_t *ad1;
-+    int n_imap;
-+    int *imap_arr;
-+}   f9_data_t;
-+
-+double f9(double x, void *data)
-+{
-+    f9_data_t *d = data;
-+
-+    return -lod_lkl_beta_binomial(d->ad0, d->ad1, d->n_imap, d->imap_arr, x);
-+}
-+
-+static inline f9_data_t *f9_pack(int16_t *ad0, int16_t *ad1, int n_imap,
-+    int *imap_arr)
-+{
-+    f9_data_t *d = malloc(sizeof(f9_data_t));
-+
-+    d->ad0 = ad0;
-+    d->ad1 = ad1;
-+    d->n_imap = n_imap;
-+    d->imap_arr = imap_arr;
-+
-+    return d;
-+}
-+
- // this function computes several contig stats and then clears the contig data from the sample
- static void sample_stats(sample_t *self, const model_t *model) {
-     int n = self->n;
-@@ -1968,9 +2278,10 @@ static void sample_stats(sample_t *self, const model_t
-         self->x_nonpar_lrr_median = get_median(lrr, n_imap, imap_arr);
- 
-         if (model->flags & WGS_DATA) {
--            double f(double x, void *data) { return -lod_lkl_beta_binomial(ad0, ad1, n_imap, imap_arr, x); }
-+            f9_data_t *f9_data = f9_pack(ad0, ad1, n_imap, imap_arr);
-             double x;
--            kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &x); // dispersions above 0.5 are not allowed
-+            kmin_brent(f9, 0.1, 0.2, f9_data, KMIN_EPS, &x); // dispersions above 0.5 are not allowed
-+	    free(f9_data);
-             self->x_nonpar_dispersion = (float)x;
-         } else {
-             self->x_nonpar_dispersion = get_sample_sd(baf, n_imap, imap_arr);
-@@ -1995,9 +2306,10 @@ static void sample_stats(sample_t *self, const model_t
-         hts_expand(stats_t, self->n_stats, self->m_stats, self->stats_arr);
- 
-         if (model->flags & WGS_DATA) {
--            double f(double x, void *data) { return -lod_lkl_beta_binomial(ad0, ad1, n, NULL, x); }
-             double x;
--            kmin_brent(f, 0.1, 0.2, NULL, KMIN_EPS, &x); // dispersions above 0.5 are not allowed
-+	    f2_data_t *f2_data = f2_pack(ad0, ad1, n);
-+            kmin_brent(f2, 0.1, 0.2, f2_data, KMIN_EPS, &x); // dispersions above 0.5 are not allowed
-+	    free(f2_data);
-             self->stats_arr[self->n_stats - 1].dispersion = (float)x;
-         } else {
-             self->stats_arr[self->n_stats - 1].dispersion = get_sample_sd(baf, n, NULL);
diff --git a/biology/bio-mocha/pkg-plist b/biology/bio-mocha/pkg-plist
index b7be082bf4e3..4604936e8e0f 100644
--- a/biology/bio-mocha/pkg-plist
+++ b/biology/bio-mocha/pkg-plist
@@ -3,7 +3,7 @@ libexec/bcftools/mocha.so
 libexec/bcftools/mochatools.so
 libexec/bcftools/score.so
 libexec/bcftools/trio-phase.so
+%%DATADIR%%/assoc_plot.R
 %%DATADIR%%/mocha_plot.R
 %%DATADIR%%/pileup_plot.R
-%%DATADIR%%/shift_plot.R
 %%DATADIR%%/summary_plot.R