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comparison PsiCLASS-1.0.2/samtools-0.1.19/bamshuf.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
1 #include <unistd.h>
2 #include <stdio.h>
3 #include <stdlib.h>
4 #include <string.h>
5 #include <assert.h>
6 #include "sam.h"
7 #include "ksort.h"
8
9 #define DEF_CLEVEL 1
10
11 static inline unsigned hash_Wang(unsigned key)
12 {
13 key += ~(key << 15);
14 key ^= (key >> 10);
15 key += (key << 3);
16 key ^= (key >> 6);
17 key += ~(key << 11);
18 key ^= (key >> 16);
19 return key;
20 }
21
22 static inline unsigned hash_X31_Wang(const char *s)
23 {
24 unsigned h = *s;
25 if (h) {
26 for (++s ; *s; ++s) h = (h << 5) - h + *s;
27 return hash_Wang(h);
28 } else return 0;
29 }
30
31 typedef struct {
32 unsigned key;
33 bam1_t *b;
34 } elem_t;
35
36 static inline int elem_lt(elem_t x, elem_t y)
37 {
38 if (x.key < y.key) return 1;
39 if (x.key == y.key) {
40 int t;
41 t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b));
42 if (t < 0) return 1;
43 return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3)));
44 } else return 0;
45 }
46
47 KSORT_INIT(bamshuf, elem_t, elem_lt)
48
49 static void bamshuf(const char *fn, int n_files, const char *pre, int clevel, int is_stdout)
50 {
51 BGZF *fp, *fpw, **fpt;
52 char **fnt, modew[8];
53 bam1_t *b;
54 int i, l;
55 bam_hdr_t *h;
56 int64_t *cnt;
57
58 // split
59 fp = strcmp(fn, "-")? bgzf_open(fn, "r") : bgzf_dopen(fileno(stdin), "r");
60 assert(fp);
61 h = bam_hdr_read(fp);
62 fnt = (char**)calloc(n_files, sizeof(void*));
63 fpt = (BGZF**)calloc(n_files, sizeof(void*));
64 cnt = (int64_t*)calloc(n_files, 8);
65 l = strlen(pre);
66 for (i = 0; i < n_files; ++i) {
67 fnt[i] = (char*)calloc(l + 10, 1);
68 sprintf(fnt[i], "%s.%.4d.bam", pre, i);
69 fpt[i] = bgzf_open(fnt[i], "w1");
70 bam_hdr_write(fpt[i], h);
71 }
72 b = bam_init1();
73 while (bam_read1(fp, b) >= 0) {
74 uint32_t x;
75 x = hash_X31_Wang(bam_get_qname(b)) % n_files;
76 bam_write1(fpt[x], b);
77 ++cnt[x];
78 }
79 bam_destroy1(b);
80 for (i = 0; i < n_files; ++i) bgzf_close(fpt[i]);
81 free(fpt);
82 bgzf_close(fp);
83 // merge
84 sprintf(modew, "w%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
85 if (!is_stdout) { // output to a file
86 char *fnw = (char*)calloc(l + 5, 1);
87 sprintf(fnw, "%s.bam", pre);
88 fpw = bgzf_open(fnw, modew);
89 free(fnw);
90 } else fpw = bgzf_dopen(fileno(stdout), modew); // output to stdout
91 bam_hdr_write(fpw, h);
92 bam_hdr_destroy(h);
93 for (i = 0; i < n_files; ++i) {
94 int64_t j, c = cnt[i];
95 elem_t *a;
96 fp = bgzf_open(fnt[i], "r");
97 bam_hdr_destroy(bam_hdr_read(fp));
98 a = (elem_t*)calloc(c, sizeof(elem_t));
99 for (j = 0; j < c; ++j) {
100 a[j].b = bam_init1();
101 assert(bam_read1(fp, a[j].b) >= 0);
102 a[j].key = hash_X31_Wang(bam_get_qname(a[j].b));
103 }
104 bgzf_close(fp);
105 unlink(fnt[i]);
106 free(fnt[i]);
107 ks_introsort(bamshuf, c, a);
108 for (j = 0; j < c; ++j) {
109 bam_write1(fpw, a[j].b);
110 bam_destroy1(a[j].b);
111 }
112 free(a);
113 }
114 bgzf_close(fpw);
115 free(fnt); free(cnt);
116 }
117
118 int main_bamshuf(int argc, char *argv[])
119 {
120 int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0;
121 while ((c = getopt(argc, argv, "n:l:uO")) >= 0) {
122 switch (c) {
123 case 'n': n_files = atoi(optarg); break;
124 case 'l': clevel = atoi(optarg); break;
125 case 'u': is_un = 1; break;
126 case 'O': is_stdout = 1; break;
127 }
128 }
129 if (is_un) clevel = 0;
130 if (optind + 2 > argc) {
131 fprintf(stderr, "\nUsage: bamshuf [-Ou] [-n nFiles] [-c cLevel] <in.bam> <out.prefix>\n\n");
132 fprintf(stderr, "Options: -O output to stdout\n");
133 fprintf(stderr, " -u uncompressed BAM output\n");
134 fprintf(stderr, " -l INT compression level [%d]\n", DEF_CLEVEL);
135 fprintf(stderr, " -n INT number of temporary files [%d]\n", n_files);
136 fprintf(stderr, "\n");
137 return 1;
138 }
139 bamshuf(argv[optind], n_files, argv[optind+1], clevel, is_stdout);
140 return 0;
141 }