Merge commit 'upstream/0.5'

[pysam.git] / samtools / bam_mate.c.pysam.c

diff --git a/samtools/bam_mate.c.pysam.c b/samtools/bam_mate.c.pysam.c
new file mode 100644 (file)
index 0000000..ebb797b
--- /dev/null
+++ b/samtools/bam_mate.c.pysam.c
@@ -0,0 +1,72 @@
+#include "pysam.h"
+
+#include <stdlib.h>
+#include <string.h>
+#include "bam.h"
+
+// currently, this function ONLY works if each read has one hit
+void bam_mating_core(bamFile in, bamFile out)
+{
+       bam_header_t *header;
+       bam1_t *b[2];
+       int curr, has_prev;
+
+       header = bam_header_read(in);
+       bam_header_write(out, header);
+
+       b[0] = bam_init1();
+       b[1] = bam_init1();
+       curr = 0; has_prev = 0;
+       while (bam_read1(in, b[curr]) >= 0) {
+               bam1_t *cur = b[curr], *pre = b[1-curr];
+               if (has_prev) {
+                       if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
+                               cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
+                               pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
+                               if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
+                                       && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
+                               {
+                                       uint32_t cur5, pre5;
+                                       cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
+                                       pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
+                                       cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
+                               } else cur->core.isize = pre->core.isize = 0;
+                               if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
+                               else cur->core.flag &= ~BAM_FMREVERSE;
+                               if (cur->core.flag&BAM_FREVERSE) pre->core.flag |= BAM_FMREVERSE;
+                               else pre->core.flag &= ~BAM_FMREVERSE;
+                               if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
+                               if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
+                               bam_write1(out, pre);
+                               bam_write1(out, cur);
+                               has_prev = 0;
+                       } else { // unpaired or singleton
+                               pre->core.mtid = -1; pre->core.mpos = -1; pre->core.isize = 0;
+                               if (pre->core.flag & BAM_FPAIRED) {
+                                       pre->core.flag |= BAM_FMUNMAP;
+                                       pre->core.flag &= ~BAM_FMREVERSE & ~BAM_FPROPER_PAIR;
+                               }
+                               bam_write1(out, pre);
+                       }
+               } else has_prev = 1;
+               curr = 1 - curr;
+       }
+       if (has_prev) bam_write1(out, b[1-curr]);
+       bam_header_destroy(header);
+       bam_destroy1(b[0]);
+       bam_destroy1(b[1]);
+}
+
+int bam_mating(int argc, char *argv[])
+{
+       bamFile in, out;
+       if (argc < 3) {
+               fprintf(pysamerr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+               return 1;
+       }
+       in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
+    out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
+       bam_mating_core(in, out);
+       bam_close(in); bam_close(out);
+       return 0;
+}