Imported Upstream version 0.1.18

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index b2d7d4a197b112ea10c6caf3ad4a9a13d95b1298..3cc464949eb69e630ee7905c96d4f8050b1b569c 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -8,6 +8,11 @@
 #include "kstring.h"
 #include "time.h"
 
 #include "kstring.h"
 #include "time.h"
 

+#ifdef _WIN32
+#define srand48(x) srand(x)
+#define lrand48() rand()
+#endif
+

 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 16384)
 
 #include "kseq.h"
 KSTREAM_INIT(gzFile, gzread, 16384)
 


@@ -126,7 +131,6 @@ static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr,
                if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
                if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
                if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
                if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
                if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
                if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);

-               //if (em[9] >= 0) ksprintf(&s, ";LRT1=%.3g", em[9]);

        }
        if (cons_llr > 0) {
                ksprintf(&s, ";CLR=%d", cons_llr);
        }
        if (cons_llr > 0) {
                ksprintf(&s, ";CLR=%d", cons_llr);


@@ -269,6 +273,8 @@ static void write_header(bcf_hdr_t *h)
         kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
     if (!strstr(str.s, "##INFO=<ID=RP,"))
         kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
         kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
     if (!strstr(str.s, "##INFO=<ID=RP,"))
         kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);

+    if (!strstr(str.s, "##INFO=<ID=VDB,"))
+        kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);

     if (!strstr(str.s, "##FORMAT=<ID=GT,"))
         kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
     if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
     if (!strstr(str.s, "##FORMAT=<ID=GT,"))
         kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
     if (!strstr(str.s, "##FORMAT=<ID=GQ,"))


@@ -280,7 +286,7 @@ static void write_header(bcf_hdr_t *h)
        if (!strstr(str.s, "##FORMAT=<ID=SP,"))
                kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
        if (!strstr(str.s, "##FORMAT=<ID=PL,"))
        if (!strstr(str.s, "##FORMAT=<ID=SP,"))
                kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
        if (!strstr(str.s, "##FORMAT=<ID=PL,"))

-               kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+               kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);

        h->l_txt = str.l + 1; h->txt = str.s;
 }
 
        h->l_txt = str.l + 1; h->txt = str.s;
 }
 


@@ -490,7 +496,7 @@ int bcfview(int argc, char *argv[])
                        if (!(l > begin && end > b->pos)) continue;
                }
                ++n_processed;
                        if (!(l > begin && end > b->pos)) continue;
                }
                ++n_processed;

-               if (vc.flag & VC_QCNT) { // summarize the difference
+               if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference

                        int x = bcf_min_diff(b);
                        if (x > 255) x = 255;
                        if (x >= 0) ++qcnt[x];
                        int x = bcf_min_diff(b);
                        if (x > 255) x = 255;
                        if (x >= 0) ++qcnt[x];