From: Heng Li <lh3@live.co.uk>
Date: Fri, 23 Jul 2010 01:39:13 +0000 (+0000)
Subject:  * samtools-0.1.8-3 (r627)
X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=commitdiff_plain;h=d763698cc12d7daa7361d610db3c9c9e83e7655b

 * samtools-0.1.8-3 (r627)
 * multi-sample snp calling appears to work. More tests needed.
---

diff --git a/bam_mcns.c b/bam_mcns.c
index cd64b0a..dee2016 100644
--- a/bam_mcns.c
+++ b/bam_mcns.c
@@ -12,7 +12,7 @@ struct __mc_aux_t {
 	double theta;
 	double *q2p, *pdg; // pdg -> P(D|g)
 	double *alpha, *beta;
-	int *qsum, *bcnt, rcnt[4];
+	int *qsum, *bcnt;
 };
 
 void mc_init_prior(mc_aux_t *ma, double theta)
@@ -65,11 +65,9 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
 	int i, j;
 	memset(ma->qsum, 0, sizeof(int) * 4 * ma->n);
 	memset(ma->bcnt, 0, sizeof(int) * 4 * ma->n);
-	memset(ma->rcnt, 0, sizeof(int) * 4);
 	for (j = 0; j < ma->n; ++j) {
 		int tmp, *qsum = ma->qsum + j * 4;
 		int *bcnt = ma->bcnt + j * 4;
-		double r = drand48(), rr;
 		for (i = tmp = 0; i < n[j]; ++i) {
 			const bam_pileup1_t *p = plp[j] + i;
 			int q, b;
@@ -83,13 +81,6 @@ static void sum_err(int *n, const bam_pileup1_t **plp, mc_aux_t *ma)
 			++bcnt[b];
 			++tmp;
 		}
-		if (tmp) {
-			for (i = 0, rr = 0.; i < 4; ++i) {
-				rr += (double)bcnt[i] / tmp;
-				if (rr >= r) break;
-			}
-			if (i < 4) ++ma->rcnt[i];
-		}
 	}
 }
 
@@ -127,21 +118,21 @@ static void cal_pdg(mc_aux_t *ma)
 // return the reference allele frequency
 double mc_freq0(int ref, int *n, const bam_pileup1_t **plp, mc_aux_t *ma, int *_ref, int *alt)
 {
-	int i, acnt[4], j;
-	double fr = -1., f0 = -1.;
+	int i, cnt;
+	double f;
 	sum_err(n, plp, ma);
 	set_allele(ref, ma);
 	cal_pdg(ma);
-	acnt[0] = acnt[1] = acnt[2] = acnt[3] = 0;
-	for (i = 0; i < ma->n; ++i)
-		for (j = 0; j < 4; ++j)
-			acnt[j] += ma->bcnt[i * 4 + j];
-	if (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]) // never used...
-		fr = (double)ma->rcnt[ref] / (ma->rcnt[ma->ref] + ma->rcnt[ma->alt]);
-	if (acnt[ma->ref] + acnt[ma->alt])
-		f0 = (double)acnt[ref] / (acnt[ma->ref] + acnt[ma->alt]);
 	*_ref = ma->ref; *alt = ma->alt;
-	return ma->n == 1 || fr < 0.? f0 : fr;
+	for (i = cnt = 0, f = 0.; i < ma->n; ++i) {
+		int *bcnt = ma->bcnt + i * 4;
+		int x = bcnt[ma->ref] + bcnt[ma->alt];
+		if (x) {
+			++cnt;
+			f += (double)bcnt[ma->ref] / x;
+		}
+	}
+	return f / cnt;
 }
 // f0 is the reference allele frequency
 double mc_freq_iter(double f0, mc_aux_t *ma)
diff --git a/bam_plcmd.c b/bam_plcmd.c
index 2854770..2afebea 100644
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -557,11 +557,13 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 			f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
 			if (f >= 0.0) {
 				double q, flast = f;
-				for (j = 0; j < 10; ++j){
+				for (j = 0; j < 10; ++j) {
 					f = mc_freq_iter(flast, ma);
+//					printf("%lg->%lg\n", flast, f);
 					if (fabs(f - flast) < 1e-3) break;
 					flast = f;
 				}
+				if (1. - f < 1e-4) f = 1.;
 				pref = mc_ref_prob(ma);
 				is_var = (pref < .5);
 				q = is_var? pref : 1. - pref;
@@ -655,7 +657,17 @@ int bam_mpileup(int argc, char *argv[])
 		}
 	}
 	if (argc == 1) {
-		fprintf(stderr, "Usage: samtools mpileup [-r reg] [-f in.fa] [-l pos] in1.bam [in2.bam [...]]\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+		fprintf(stderr, "Options: -f FILE     reference sequence file [null]\n");
+		fprintf(stderr, "         -r STR      region in which pileup is generated [null]\n");
+		fprintf(stderr, "         -l FILE     list of positions (format: chr pos) [null]\n");
+		fprintf(stderr, "         -M INT      cap mapping quality at INT [%d]\n", mplp.max_mq);
+		fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
+		fprintf(stderr, "         -V          generate VCF output (SNP calling)\n");
+		fprintf(stderr, "         -v          show variant sites only\n");
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Notes: Assuming error independency and diploid individuals.\n\n");
 		return 1;
 	}
 	mpileup(&mplp, argc - optind, argv + optind);
diff --git a/bamtk.c b/bamtk.c
index b5f6b67..b51df96 100644
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8-2 (r617)"
+#define PACKAGE_VERSION "0.1.8-3 (r627)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);