Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM...

[rsem.git] / scanForPairedEndReads.cpp

diff --git a/scanForPairedEndReads.cpp b/scanForPairedEndReads.cpp
new file mode 100644 (file)
index 0000000..4d1fbfb
--- /dev/null
+++ b/scanForPairedEndReads.cpp
@@ -0,0 +1,120 @@
+#include<cstdio>
+#include<cstring>
+#include<cstdlib>
+#include<cassert>
+#include<string>
+#include<vector>
+#include<algorithm>
+
+#include <stdint.h>
+#include "sam/bam.h"
+#include "sam/sam.h"
+
+#include "my_assert.h"
+
+using namespace std;
+
+samfile_t *in, *out;
+bam1_t *b, *b2;
+vector<bam1_t*> arr_both, arr_partial_1, arr_partial_2, arr_partial_unknown;
+
+inline void add_to_appropriate_arr(bam1_t *b) {
+       if (!(b->core.flag & 0x0004) && (b->core.flag & 0x0002)) {
+               arr_both.push_back(bam_dup1(b)); return;
+       }
+
+       if (b->core.flag & 0x0040) arr_partial_1.push_back(bam_dup1(b));
+       else if (b->core.flag & 0x0080) arr_partial_2.push_back(bam_dup1(b));
+       else arr_partial_unknown.push_back(bam_dup1(b));
+}
+
+bool less_than(bam1_t *a, bam1_t *b) {
+       int32_t ap1 = min(a->core.pos, a->core.mpos);
+       int32_t ap2 = max(a->core.pos, a->core.mpos);
+       int32_t bp1 = min(b->core.pos, b->core.mpos);
+       int32_t bp2 = max(b->core.pos, b->core.mpos);
+
+       if (a->core.tid != b->core.tid) return a->core.tid < b->core.tid;
+       if (ap1 != bp1) return ap1 < bp1;
+       return ap2 < bp2;
+}
+
+int main(int argc, char* argv[]) {
+       if (argc != 3) {
+               printf("Usage: rsem-scan-for-paired-end-reads input.sam output.bam\n");
+               exit(-1);
+       }
+
+       in = samopen(argv[1], "r", NULL);
+       general_assert(in != 0, "Cannot open " + cstrtos(argv[1]) + " !");
+       out = samopen(argv[2], "wb", in->header);
+       general_assert(out != 0, "Cannot open " + cstrtos(argv[2]) + " !");
+
+       b = bam_init1(); b2 = bam_init1();
+
+       string qname;
+       bool go_on = (samread(in, b) >= 0);
+       bool isPaired;
+       long cnt = 0;
+
+       printf("."); fflush(stdout);
+
+       while (go_on) {
+               qname.assign(bam1_qname(b));
+               isPaired = (b->core.flag & 0x0001);
+
+               if (isPaired) {
+                       add_to_appropriate_arr(b);
+                       while ((go_on = (samread(in, b) >= 0)) && (qname == bam1_qname(b))) {
+                               general_assert(b->core.flag & 0x0001, "Read " + qname + " is detected as both single-end and paired-end read!", true);
+                               add_to_appropriate_arr(b);
+                       }
+
+                       general_assert(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!", true);
+                       general_assert((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!", true);
+
+                       if (!arr_both.empty()) {
+                               sort(arr_both.begin(), arr_both.end(), less_than);
+                               for (size_t i = 0; i < arr_both.size(); i++) { samwrite(out, arr_both[i]); bam_destroy1(arr_both[i]); }
+                               arr_both.clear();
+                       }
+
+                       while (!arr_partial_1.empty() || !arr_partial_2.empty()) {
+                               if (!arr_partial_1.empty() && !arr_partial_2.empty()) {
+                                       samwrite(out, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back();
+                                       samwrite(out, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back();
+                               }
+                               else if (!arr_partial_1.empty()) {
+                                       samwrite(out, arr_partial_1.back()); bam_destroy1(arr_partial_1.back()); arr_partial_1.pop_back();
+                                       samwrite(out, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back();
+                               }
+                               else {
+                                       samwrite(out, arr_partial_2.back()); bam_destroy1(arr_partial_2.back()); arr_partial_2.pop_back();
+                                       samwrite(out, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back();
+                               }
+                       }
+
+                       while (!arr_partial_unknown.empty()) {
+                               samwrite(out, arr_partial_unknown.back()); bam_destroy1(arr_partial_unknown.back()); arr_partial_unknown.pop_back();
+                       }
+               }
+               else {
+                       samwrite(out, b);
+                       while ((go_on = (samread(in, b) >= 0)) && (qname == bam1_qname(b))) {
+                               samwrite(out, b);
+                       }
+               }
+
+               ++cnt;
+               if (cnt % 1000000 == 0) { printf("."); fflush(stdout); }
+       }
+
+       printf("\nFinished!\n");
+
+       bam_destroy1(b); bam_destroy1(b2);
+
+       samclose(in);
+       samclose(out);
+
+       return 0;
+}