git: e33f72037a79 - main - biology/bio-mocha: Update to 1.14-20220112
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Date: Thu, 13 Jan 2022 19:00:43 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=e33f72037a797431e5c4d89d1d222c5d5d92eb27
commit e33f72037a797431e5c4d89d1d222c5d5d92eb27
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-01-13 18:58:35 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-01-13 19:00:41 +0000
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.
---
biology/bio-mocha/Makefile | 5 +-
biology/bio-mocha/distinfo | 10 +-
.../bio-mocha/files/patch-plugins_beta__binom.h | 19 -
biology/bio-mocha/files/patch-plugins_mocha.c | 479 ---------------------
biology/bio-mocha/pkg-plist | 2 +-
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