+------------------------------------------------------------------------
+r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/bam_stat.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.2-1
+ * added flagstat command
+
+------------------------------------------------------------------------
+r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/samtools.1
+
+Release SAMtools-0.1.2
+
------------------------------------------------------------------------
r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
min = g3;
if (min > r->gl[0]) min = r->gl[0];
if (min > r->gl[1]) min = r->gl[1];
- g3 -= min;
g2.ref_base = 0;
g2.type = GLF_TYPE_INDEL;
memset(g2.lk, 0, 10);
- g2.lk[0] = r->gl[0] < 255? r->gl[0] : 255;
- g2.lk[1] = r->gl[1] < 255? r->gl[1] : 255;
- g2.lk[2] = g3 < 255? g3 : 255;
+ g2.lk[0] = r->gl[0] - min < 255? r->gl[0] - min : 255;
+ g2.lk[1] = r->gl[1] - min < 255? r->gl[1] - min : 255;
+ g2.lk[2] = g3 - min < 255? g3 - min : 255;
*(int16_t*)(g2.lk + 3) = (int16_t)r->indel1;
*(int16_t*)(g2.lk + 5) = (int16_t)r->indel2;
g2.min_lk = min < 255? min : 255;
printf("%lld in total\n", s->n_reads);
printf("%lld QC failure\n", s->n_qcfail);
printf("%lld duplicates\n", s->n_dup);
- printf("%lld mapped\n", s->n_mapped);
+ printf("%lld mapped (%.2f%%)\n", s->n_mapped, (float)s->n_mapped / s->n_reads * 100.0);
printf("%lld paired in sequencing\n", s->n_pair_all);
printf("%lld read1\n", s->n_read1);
printf("%lld read2\n", s->n_read2);
- printf("%lld properly paired\n", s->n_pair_good);
- printf("%lld with both itself and its mate mapped\n", s->n_pair_map);
- printf("%lld singletons\n", s->n_sgltn);
- printf("%lld with its mate mapped to a different chr\n", s->n_diffchr);
+ printf("%lld properly paired (%.2f%%)\n", s->n_pair_good, (float)s->n_pair_good / s->n_reads * 100.0);
+ printf("%lld with itself and mate mapped\n", s->n_pair_map);
+ printf("%lld singletons (%.2f%%)\n", s->n_sgltn, (float)s->n_sgltn / s->n_reads * 100.0);
+ printf("%lld with mate mapped to a different chr\n", s->n_diffchr);
+ printf("%lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh);
free(s);
bam_header_destroy(header);
bam_close(fp);
#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-1"
+#define PACKAGE_VERSION "0.1.2-3"
#endif
int bam_taf2baf(int argc, char *argv[]);