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in repository wgsim.
commit e33dee6300feb5ab2c5c4cbf9f6d13767cfcfba1
Author: Kevin Murray <s...@kdmurray.id.au>
Date: Sat Jul 4 20:09:58 2015 +1000
Imported Upstream version 0.3.1-r13
---
.gitignore | 1 +
README | 93 +++++++++++++
kseq.h | 225 ++++++++++++++++++++++++++++++
wgsim.c | 437 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
wgsim_eval.pl | 294 +++++++++++++++++++++++++++++++++++++++
5 files changed, 1050 insertions(+)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..a01ee28
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.*.swp
diff --git a/README b/README
new file mode 100644
index 0000000..3b3f105
--- /dev/null
+++ b/README
@@ -0,0 +1,93 @@
+Introduction
+============
+
+Wgsim is a small tool for simulating sequence reads from a reference genome.
+It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL)
+polymorphisms, and simulate reads with uniform substitution sequencing errors.
+It does not generate INDEL sequencing errors, but this can be partly
+compensated by simulating INDEL polymorphisms.
+
+Wgsim outputs the simulated polymorphisms, and writes the true read coordinates
+as well as the number of polymorphisms and sequencing errors in read names.
+One can evaluate the accuracy of a mapper or a SNP caller with wgsim_eval.pl
+that comes with the package.
+
+
+Compilation
+===========
+
+gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm
+
+
+History
+=======
+
+Wgsim was modified from MAQ's read simulator by dropping dependencies to other
+source codes in the MAQ package and incorporating patches from Colin Hercus
+which allow to simulate INDELs longer than 1bp. Wgsim was originally released
+in the SAMtools software package. I forked it out in 2011 as a standalone
+project. A few improvements were also added in this course.
+
+
+Evaluation
+==========
+
+Simulation and evaluation
+-------------------------
+
+The command line for simulation:
+
+ wgsim -Nxxx -1yyy -d0 -S11 -e0 -rzzz hs37m.fa yyy-zzz.fq /dev/null
+
+where yyy is the read length, zzz is the error rate and $xxx * $yyy = 10000000.
+By default, 15% of polymorphisms are INDELs and their lengths are drawn from a
+geometric distribution with density 0.7*0.3^{l-1}.
+
+The command line for evaluation:
+
+ wgsim_eval.pl unique aln.sam | wgsim_eval.pl alneval -g 20
+
+The '-g' option may be changed with mappers.
+
+
+System
+------
+
+GCC: 4.1.2
+CPU: AMD Opteron 8350 @ 2.0GHz
+Mem: 128GB
+
+
+Results
+-------
+
+==================================================================================================================
+ 100bp 200bp 500bp
1000bp 10000bp
+ ------------------ ----------------- -----------------
----------------- -----------------
+ Program Metrics 2% 5% 10% 2% 5% 10% 2% 5% 10%
2% 5% 10% 2% 5% 10%
+------------------------------------------------------------------------------------------------------------------
+ CPU 249 198 136 325 262 163 332 243 232
320 235 215 235 197 189
+ BWA-SW Q20% 85.1 63.6 21.4 93.7 88.9 53.5 96.4 95.7 89.2
96.6 96.2 95.1 97.7 98.3 97.7
+ err% 0.01 0.06 0.20 0.00 0.01 0.14 0.00 0.01 0.01
0.00 0.00 0.01 0.00 0.00 0.00
+ one% 94.6 77.4 35.7 97.5 95.1 67.6 98.6 98.5 93.4
99.0 98.9 98.3 99.7 99.8 99.7
+------------------------------------------------------------------------------------------------------------------
+ CPU 302 484 1060
330 352 607 381 480 919
+ AGILE Q20% 98.6 98.4 98.4
98.4 98.4 98.6 98.2 98.6 99.3
+ err% 0.66 0.69 2.31
0.34 0.40 0.70 0.10 0.00 0.20
+ one% 100 99.4 0
100 100 100 100 100 100
+==================================================================================================================
+
+1) AGILE throws "Floating point exception" halfway for 100/200bp reads. The
+ default output is supposed to be PSL, but actually has an additional "score"
+ column. AGILE is reportedly faster than BWA-SW for 1000bp reads. It is
+ slower here possibly because of suboptimal command line options.
+
+2) Gassst uses over 27GB memory in 20 minutes. The memory then quickly
+ increases to over 40GB. It gets killed.
+
+3) Lastz complains: "FAILURE: bad fasta character in hs37m.fa ...".
+
+4) Pash only gives 'unique mapping'. Its unique mapping is better than BWA-SW's
+ Q1 mapiping. It is very slow, though, possibly because of suboptimal
+ options.
+
diff --git a/kseq.h b/kseq.h
new file mode 100644
index 0000000..5ba985e
--- /dev/null
+++ b/kseq.h
@@ -0,0 +1,225 @@
+/* The MIT License
+
+ Copyright (c) 2008, 2009 Attractive Chaos <attrac...@live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/*
+ 2009-07-16 (lh3): in kstream_t, change "char*" to "unsigned char*"
+ */
+
+/* Last Modified: 12APR2009 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB 1 // isspace() && !' '
+#define KS_SEP_MAX 1
+
+#define __KS_TYPE(type_t) \
+ typedef struct __kstream_t { \
+ unsigned char *buf;
\
+ int begin, end, is_eof; \
+ type_t f;
\
+ } kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize)
\
+ static inline kstream_t *ks_init(type_t f)
\
+ {
\
+ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));
\
+ ks->f = f;
\
+ ks->buf = malloc(__bufsize);
\
+ return ks;
\
+ }
\
+ static inline void ks_destroy(kstream_t *ks)
\
+ {
\
+ if (ks) {
\
+ free(ks->buf);
\
+ free(ks);
\
+ }
\
+ }
+
+#define __KS_GETC(__read, __bufsize)
\
+ static inline int ks_getc(kstream_t *ks)
\
+ {
\
+ if (ks->is_eof && ks->begin >= ks->end) return -1; \
+ if (ks->begin >= ks->end) {
\
+ ks->begin = 0;
\
+ ks->end = __read(ks->f, ks->buf, __bufsize); \
+ if (ks->end < __bufsize) ks->is_eof = 1;
\
+ if (ks->end == 0) return -1;
\
+ }
\
+ return (int)ks->buf[ks->begin++];
\
+ }
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4,
(x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize)
\
+ static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str,
int *dret) \
+ {
\
+ if (dret) *dret = 0;
\
+ str->l = 0;
\
+ if (ks->begin >= ks->end && ks->is_eof) return -1;
\
+ for (;;) {
\
+ int i;
\
+ if (ks->begin >= ks->end) {
\
+ if (!ks->is_eof) {
\
+ ks->begin = 0;
\
+ ks->end = __read(ks->f, ks->buf,
__bufsize); \
+ if (ks->end < __bufsize) ks->is_eof =
1; \
+ if (ks->end == 0) break;
\
+ } else break;
\
+ }
\
+ if (delimiter > KS_SEP_MAX) {
\
+ for (i = ks->begin; i < ks->end; ++i)
\
+ if (ks->buf[i] == delimiter) break;
\
+ } else if (delimiter == KS_SEP_SPACE) {
\
+ for (i = ks->begin; i < ks->end; ++i)
\
+ if (isspace(ks->buf[i])) break;
\
+ } else if (delimiter == KS_SEP_TAB) {
\
+ for (i = ks->begin; i < ks->end; ++i)
\
+ if (isspace(ks->buf[i]) && ks->buf[i]
!= ' ') break; \
+ } else i = 0; /* never come to here! */
\
+ if (str->m - str->l < i - ks->begin + 1) {
\
+ str->m = str->l + (i - ks->begin) + 1;
\
+ kroundup32(str->m);
\
+ str->s = (char*)realloc(str->s, str->m);
\
+ }
\
+ memcpy(str->s + str->l, ks->buf + ks->begin, i -
ks->begin); \
+ str->l = str->l + (i - ks->begin);
\
+ ks->begin = i + 1;
\
+ if (i < ks->end) {
\
+ if (dret) *dret = ks->buf[i];
\
+ break;
\
+ }
\
+ }
\
+ if (str->l == 0) {
\
+ str->m = 1;
\
+ str->s = (char*)calloc(1, 1);
\
+ }
\
+ str->s[str->l] = '\0';
\
+ return str->l;
\
+ }
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+ __KS_TYPE(type_t)
\
+ __KS_BASIC(type_t, __bufsize) \
+ __KS_GETC(__read, __bufsize) \
+ __KS_GETUNTIL(__read, __bufsize)
+
+#define __KSEQ_BASIC(type_t)
\
+ static inline kseq_t *kseq_init(type_t fd)
\
+ {
\
+ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));
\
+ s->f = ks_init(fd);
\
+ return s;
\
+ }
\
+ static inline void kseq_rewind(kseq_t *ks)
\
+ {
\
+ ks->last_char = 0;
\
+ ks->f->is_eof = ks->f->begin = ks->f->end = 0;
\
+ }
\
+ static inline void kseq_destroy(kseq_t *ks)
\
+ {
\
+ if (!ks) return;
\
+ free(ks->name.s); free(ks->comment.s); free(ks->seq.s);
free(ks->qual.s); \
+ ks_destroy(ks->f);
\
+ free(ks);
\
+ }
+
+/* Return value:
+ >=0 length of the sequence (normal)
+ -1 end-of-file
+ -2 truncated quality string
+ */
+#define __KSEQ_READ
\
+ static int kseq_read(kseq_t *seq)
\
+ {
\
+ int c;
\
+ kstream_t *ks = seq->f;
\
+ if (seq->last_char == 0) { /* then jump to the next header line
*/ \
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c !=
'@'); \
+ if (c == -1) return -1; /* end of file */
\
+ seq->last_char = c;
\
+ } /* the first header char has been read */
\
+ seq->comment.l = seq->seq.l = seq->qual.l = 0;
\
+ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1;
\
+ if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0);
\
+ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c !=
'@') { \
+ if (isgraph(c)) { /* printable non-space character */
\
+ if (seq->seq.l + 1 >= seq->seq.m) { /* double
the memory */ \
+ seq->seq.m = seq->seq.l + 2;
\
+ kroundup32(seq->seq.m); /* rounded to
next closest 2^k */ \
+ seq->seq.s = (char*)realloc(seq->seq.s,
seq->seq.m); \
+ }
\
+ seq->seq.s[seq->seq.l++] = (char)c;
\
+ }
\
+ }
\
+ if (c == '>' || c == '@') seq->last_char = c; /* the first
header char has been read */ \
+ seq->seq.s[seq->seq.l] = 0; /* null terminated string */
\
+ if (c != '+') return seq->seq.l; /* FASTA */
\
+ if (seq->qual.m < seq->seq.m) { /* allocate enough memory */
\
+ seq->qual.m = seq->seq.m;
\
+ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m);
\
+ }
\
+ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest
of '+' line */ \
+ if (c == -1) return -2; /* we should not stop here */
\
+ while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l)
\
+ if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] =
(unsigned char)c; \
+ seq->qual.s[seq->qual.l] = 0; /* null terminated string */
\
+ seq->last_char = 0; /* we have not come to the next header
line */ \
+ if (seq->seq.l != seq->qual.l) return -2; /* qual string is
shorter than seq string */ \
+ return seq->seq.l;
\
+ }
+
+#define __KSEQ_TYPE(type_t) \
+ typedef struct {
\
+ kstring_t name, comment, seq, qual; \
+ int last_char;
\
+ kstream_t *f;
\
+ } kseq_t;
+
+#define KSEQ_INIT(type_t, __read) \
+ KSTREAM_INIT(type_t, __read, 4096) \
+ __KSEQ_TYPE(type_t)
\
+ __KSEQ_BASIC(type_t) \
+ __KSEQ_READ
+
+#endif
diff --git a/wgsim.c b/wgsim.c
new file mode 100644
index 0000000..5c82192
--- /dev/null
+++ b/wgsim.c
@@ -0,0 +1,437 @@
+/* The MIT License
+
+ Copyright (c) 2008 Genome Research Ltd (GRL).
+ 2011 Heng Li <l...@live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* This program is separated from maq's read simulator with Colin
+ * Hercus' modification to allow longer indels. */
+
+#include <stdlib.h>
+#include <math.h>
+#include <time.h>
+#include <assert.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <ctype.h>
+#include <string.h>
+#include <zlib.h>
+#include "kseq.h"
+KSEQ_INIT(gzFile, gzread)
+
+#define PACKAGE_VERSION "0.3.1-r13"
+
+const uint8_t nst_nt4_table[256] = {
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5 /*'-'*/, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
+};
+
+/* Simple normal random number generator, copied from genran.c */
+
+double ran_normal()
+{
+ static int iset = 0;
+ static double gset;
+ double fac, rsq, v1, v2;
+ if (iset == 0) {
+ do {
+ v1 = 2.0 * drand48() - 1.0;
+ v2 = 2.0 * drand48() - 1.0;
+ rsq = v1 * v1 + v2 * v2;
+ } while (rsq >= 1.0 || rsq == 0.0);
+ fac = sqrt(-2.0 * log(rsq) / rsq);
+ gset = v1 * fac;
+ iset = 1;
+ return v2 * fac;
+ } else {
+ iset = 0;
+ return gset;
+ }
+}
+
+/* wgsim */
+
+enum muttype_t {NOCHANGE = 0, INSERT = 0x1000, SUBSTITUTE = 0xe000, DELETE =
0xf000};
+typedef unsigned short mut_t;
+static mut_t mutmsk = (mut_t)0xf000;
+
+typedef struct {
+ int l, m; /* length and maximum buffer size */
+ mut_t *s; /* sequence */
+} mutseq_t;
+
+static double ERR_RATE = 0.02;
+static double MUT_RATE = 0.001;
+static double INDEL_FRAC = 0.15;
+static double INDEL_EXTEND = 0.3;
+static double MAX_N_RATIO = 0.05;
+
+void wgsim_mut_diref(const kseq_t *ks, int is_hap, mutseq_t *hap1, mutseq_t
*hap2)
+{
+ int i, deleting = 0;
+ mutseq_t *ret[2];
+
+ ret[0] = hap1; ret[1] = hap2;
+ ret[0]->l = ks->seq.l; ret[1]->l = ks->seq.l;
+ ret[0]->m = ks->seq.m; ret[1]->m = ks->seq.m;
+ ret[0]->s = (mut_t *)calloc(ks->seq.m, sizeof(mut_t));
+ ret[1]->s = (mut_t *)calloc(ks->seq.m, sizeof(mut_t));
+ for (i = 0; i != ks->seq.l; ++i) {
+ int c;
+ c = ret[0]->s[i] = ret[1]->s[i] =
(mut_t)nst_nt4_table[(int)ks->seq.s[i]];
+ if (deleting) {
+ if (drand48() < INDEL_EXTEND) {
+ if (deleting & 1) ret[0]->s[i] |= DELETE;
+ if (deleting & 2) ret[1]->s[i] |= DELETE;
+ continue;
+ } else deleting = 0;
+ }
+ if (c < 4 && drand48() < MUT_RATE) { // mutation
+ if (drand48() >= INDEL_FRAC) { // substitution
+ double r = drand48();
+ c = (c + (int)(r * 3.0 + 1)) & 3;
+ if (is_hap || drand48() < 0.333333) { // hom
+ ret[0]->s[i] = ret[1]->s[i] =
SUBSTITUTE|c;
+ } else { // het
+ ret[drand48()<0.5?0:1]->s[i] =
SUBSTITUTE|c;
+ }
+ } else { // indel
+ if (drand48() < 0.5) { // deletion
+ if (is_hap || drand48() < 0.333333) {
// hom-del
+ ret[0]->s[i] = ret[1]->s[i] =
DELETE;
+ deleting = 3;
+ } else { // het-del
+ deleting = drand48()<0.5?1:2;
+ ret[deleting-1]->s[i] = DELETE;
+ }
+ } else { // insertion
+ int num_ins = 0, ins = 0;
+ do {
+ num_ins++;
+ ins = (ins << 2) | (int)(drand48() * 4.0);
+ } while (num_ins < 4 && drand48() < INDEL_EXTEND);
+
+ if (is_hap || drand48() < 0.333333) {
// hom-ins
+ ret[0]->s[i] = ret[1]->s[i] =
(num_ins << 12) | (ins << 4) | c;
+ } else { // het-ins
+ ret[drand48()<0.5?0:1]->s[i] =
(num_ins << 12) | (ins << 4) | c;
+ }
+ }
+ }
+ }
+ }
+}
+void wgsim_print_mutref(const char *name, const kseq_t *ks, mutseq_t *hap1,
mutseq_t *hap2)
+{
+ int i, j = 0; // j keeps the end of the last deletion
+ for (i = 0; i != ks->seq.l; ++i) {
+ int c[3];
+ c[0] = nst_nt4_table[(int)ks->seq.s[i]];
+ c[1] = hap1->s[i]; c[2] = hap2->s[i];
+ if (c[0] >= 4) continue;
+ if ((c[1] & mutmsk) != NOCHANGE || (c[2] & mutmsk) != NOCHANGE)
{
+ if (c[1] == c[2]) { // hom
+ if ((c[1]&mutmsk) == SUBSTITUTE) { //
substitution
+ printf("%s\t%d\t%c\t%c\t-\n", name,
i+1, "ACGTN"[c[0]], "ACGTN"[c[1]&0xf]);
+ } else if ((c[1]&mutmsk) == DELETE) { // del
+ if (i >= j) {
+ printf("%s\t%d\t", name, i+1);
+ for (j = i; j < ks->seq.l &&
hap1->s[j] == hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j)
+
putchar("ACGTN"[nst_nt4_table[(int)ks->seq.s[j]]]);
+ printf("\t-\t-\n");
+ }
+ } else if (((c[1] & mutmsk) >> 12) <= 4) { //
ins
+ printf("%s\t%d\t-\t", name, i+1);
+ int n = (c[1]&mutmsk) >> 12, ins = c[1] >> 4;
+ while (n > 0) {
+ putchar("ACGTN"[ins & 0x3]);
+ ins >>= 2;
+ n--;
+ }
+ printf("\t-\n");
+ } // else: deleted base in a long deletion
+ } else { // het
+ if ((c[1]&mutmsk) == SUBSTITUTE ||
(c[2]&mutmsk) == SUBSTITUTE) { // substitution
+ printf("%s\t%d\t%c\t%c\t+\n", name,
i+1, "ACGTN"[c[0]], "XACMGRSVTWYHKDBN"[1<<(c[1]&0x3)|1<<(c[2]&0x3)]);
+ } else if ((c[1]&mutmsk) == DELETE) {
+ if (i >= j) {
+ printf("%s\t%d\t", name, i+1);
+ for (j = i; j < ks->seq.l &&
hap1->s[j] != hap2->s[j] && (hap1->s[j]&mutmsk) == DELETE; ++j)
+
putchar("ACGTN"[nst_nt4_table[(int)ks->seq.s[j]]]);
+ printf("\t-\t-\n");
+ }
+ } else if ((c[2]&mutmsk) == DELETE) {
+ if (i >= j) {
+ printf("%s\t%d\t", name, i+1);
+ for (j = i; j < ks->seq.l &&
hap1->s[j] != hap2->s[j] && (hap2->s[j]&mutmsk) == DELETE; ++j)
+
putchar("ACGTN"[nst_nt4_table[(int)ks->seq.s[j]]]);
+ printf("\t-\t-\n");
+ }
+ } else if (((c[1] & mutmsk) >> 12) <= 4 &&
((c[1] & mutmsk) >> 12) > 0) { // ins1
+ printf("%s\t%d\t-\t", name, i+1);
+ int n = (c[1]&mutmsk) >> 12, ins = c[1] >> 4;
+ while (n > 0) {
+ putchar("ACGTN"[ins & 0x3]);
+ ins >>= 2;
+ n--;
+ }
+ printf("\t+\n");
+ } else if (((c[2] & mutmsk) >> 12) <= 4 ||
((c[2] & mutmsk) >> 12) > 0) { // ins2
+ printf("%s\t%d\t-\t", name, i+1);
+ int n = (c[2]&mutmsk) >> 12, ins = c[2] >> 4;
+ while (n > 0) {
+ putchar("ACGTN"[ins & 0x3]);
+ ins >>= 2;
+ n--;
+ }
+ printf("\t+\n");
+ } // else: deleted base in a long deletion
+ }
+ }
+ }
+}
+
+void wgsim_core(FILE *fpout1, FILE *fpout2, const char *fn, int is_hap,
uint64_t N, int dist, int std_dev, int size_l, int size_r)
+{
+ kseq_t *ks;
+ mutseq_t rseq[2];
+ gzFile fp_fa;
+ uint64_t tot_len, ii;
+ int i, l, n_ref;
+ char *qstr;
+ int size[2], Q, max_size;
+ uint8_t *tmp_seq[2];
+ mut_t *target;
+
+ l = size_l > size_r? size_l : size_r;
+ qstr = (char*)calloc(l+1, 1);
+ tmp_seq[0] = (uint8_t*)calloc(l+2, 1);
+ tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
+ size[0] = size_l; size[1] = size_r;
+ max_size = size_l > size_r? size_l : size_r;
+
+ Q = (ERR_RATE == 0.0)? 'I' : (int)(-10.0 * log(ERR_RATE) / log(10.0) +
0.499) + 33;
+
+ fp_fa = gzopen(fn, "r");
+ ks = kseq_init(fp_fa);
+ tot_len = n_ref = 0;
+ fprintf(stderr, "[%s] calculating the total length of the reference
sequence...\n", __func__);
+ while ((l = kseq_read(ks)) >= 0) {
+ tot_len += l;
+ ++n_ref;
+ }
+ fprintf(stderr, "[%s] %d sequences, total length: %llu\n", __func__,
n_ref, (long long)tot_len);
+ kseq_destroy(ks);
+ gzclose(fp_fa);
+
+ fp_fa = gzopen(fn, "r");
+ ks = kseq_init(fp_fa);
+ while ((l = kseq_read(ks)) >= 0) {
+ uint64_t n_pairs = (uint64_t)((long double)l / tot_len * N +
0.5);
+ if (l < dist + 3 * std_dev) {
+ fprintf(stderr, "[%s] skip sequence '%s' as it is
shorter than %d!\n", __func__, ks->name.s, dist + 3 * std_dev);
+ continue;
+ }
+
+ // generate mutations and print them out
+ wgsim_mut_diref(ks, is_hap, rseq, rseq+1);
+ wgsim_print_mutref(ks->name.s, ks, rseq, rseq+1);
+
+ for (ii = 0; ii != n_pairs; ++ii) { // the core loop
+ double ran;
+ int d, pos, s[2], is_flip = 0;
+ int n_sub[2], n_indel[2], n_err[2], ext_coor[2], j, k;
+ FILE *fpo[2];
+
+ do { // avoid boundary failure
+ ran = ran_normal();
+ ran = ran * std_dev + dist;
+ d = (int)(ran + 0.5);
+ d = d > max_size? d : max_size;
+ pos = (int)((l - d + 1) * drand48());
+ } while (pos < 0 || pos >= ks->seq.l || pos + d - 1 >=
ks->seq.l);
+
+ // flip or not
+ if (drand48() < 0.5) {
+ fpo[0] = fpout1; fpo[1] = fpout2;
+ s[0] = size[0]; s[1] = size[1];
+ } else {
+ fpo[1] = fpout1; fpo[0] = fpout2;
+ s[1] = size[0]; s[0] = size[1];
+ is_flip = 1;
+ }
+
+ // generate the read sequences
+ target = rseq[drand48()<0.5?0:1].s; // haplotype from
which the reads are generated
+ n_sub[0] = n_sub[1] = n_indel[0] = n_indel[1] =
n_err[0] = n_err[1] = 0;
+
+#define __gen_read(x, start, iter) do {
\
+ for (i = (start), k = 0, ext_coor[x] = -10; i
>= 0 && i < ks->seq.l && k < s[x]; iter) { \
+ int c = target[i], mut_type = c &
mutmsk; \
+ if (ext_coor[x] < 0) {
\
+ if (mut_type != NOCHANGE &&
mut_type != SUBSTITUTE) continue; \
+ ext_coor[x] = i;
\
+ }
\
+ if (mut_type == DELETE) ++n_indel[x];
\
+ else if (mut_type == NOCHANGE ||
mut_type == SUBSTITUTE) { \
+ tmp_seq[x][k++] = c & 0xf;
\
+ if (mut_type == SUBSTITUTE)
++n_sub[x]; \
+ } else {
\
+ int n, ins;
\
+ ++n_indel[x];
\
+ tmp_seq[x][k++] = c & 0xf;
\
+ for (n = mut_type>>12, ins =
c>>4; n > 0 && k < s[x]; --n, ins >>= 2) \
+ tmp_seq[x][k++] = ins &
0x3; \
+ }
\
+ }
\
+ if (k != s[x]) ext_coor[x] = -10;
\
+ } while (0)
+
+ __gen_read(0, pos, ++i);
+ __gen_read(1, pos + d - 1, --i);
+ for (k = 0; k < s[1]; ++k) tmp_seq[1][k] =
tmp_seq[1][k] < 4? 3 - tmp_seq[1][k] : 4; // complement
+ if (ext_coor[0] < 0 || ext_coor[1] < 0) { // fail to
generate the read(s)
+ --ii;
+ continue;
+ }
+
+ // generate sequencing errors
+ for (j = 0; j < 2; ++j) {
+ int n_n = 0;
+ for (i = 0; i < s[j]; ++i) {
+ int c = tmp_seq[j][i];
+ if (c >= 4) { // actually c should be
never larger than 4 if everything is correct
+ c = 4;
+ ++n_n;
+ } else if (drand48() < ERR_RATE) {
+ // c = (c + (int)(drand48() *
3.0 + 1)) & 3; // random sequencing errors
+ c = (c + 1) & 3; // recurrent
sequencing errors
+ ++n_err[j];
+ }
+ tmp_seq[j][i] = c;
+ }
+ if ((double)n_n / s[j] > MAX_N_RATIO) break;
+ }
+ if (j < 2) { // too many ambiguous bases on one of the
reads
+ --ii;
+ continue;
+ }
+
+ // print
+ for (j = 0; j < 2; ++j) {
+ for (i = 0; i < s[j]; ++i) qstr[i] = Q;
+ qstr[i] = 0;
+ fprintf(fpo[j],
"@%s_%u_%u_%d:%d:%d_%d:%d:%d_%llx/%d\n", ks->name.s, ext_coor[0]+1,
ext_coor[1]+1,
+ n_err[0], n_sub[0], n_indel[0],
n_err[1], n_sub[1], n_indel[1],
+ (long long)ii, j==0? is_flip+1
: 2-is_flip);
+ for (i = 0; i < s[j]; ++i)
+ fputc("ACGTN"[(int)tmp_seq[j][i]],
fpo[j]);
+ fprintf(fpo[j], "\n+\n%s\n", qstr);
+ }
+ }
+ free(rseq[0].s); free(rseq[1].s);
+ }
+ kseq_destroy(ks);
+ gzclose(fp_fa);
+ free(qstr);
+ free(tmp_seq[0]); free(tmp_seq[1]);
+}
+
+static int simu_usage()
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Program: wgsim (short read simulator)\n");
+ fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
+ fprintf(stderr, "Contact: Heng Li <l...@sanger.ac.uk>\n\n");
+ fprintf(stderr, "Usage: wgsim [options] <in.ref.fa> <out.read1.fq>
<out.read2.fq>\n\n");
+ fprintf(stderr, "Options: -e FLOAT base error rate [%.3f]\n",
ERR_RATE);
+ fprintf(stderr, " -d INT outer distance between the two
ends [500]\n");
+ fprintf(stderr, " -s INT standard deviation [50]\n");
+ fprintf(stderr, " -N INT number of read pairs
[1000000]\n");
+ fprintf(stderr, " -1 INT length of the first read
[70]\n");
+ fprintf(stderr, " -2 INT length of the second read
[70]\n");
+ fprintf(stderr, " -r FLOAT rate of mutations [%.4f]\n",
MUT_RATE);
+ fprintf(stderr, " -R FLOAT fraction of indels [%.2f]\n",
INDEL_FRAC);
+ fprintf(stderr, " -X FLOAT probability an indel is
extended [%.2f]\n", INDEL_EXTEND);
+ fprintf(stderr, " -S INT seed for random generator
[-1]\n");
+ fprintf(stderr, " -A FLOAT disgard if the fraction of
ambiguous bases higher than FLOAT [%.2f]\n", MAX_N_RATIO);
+ fprintf(stderr, " -h haplotype mode\n");
+ fprintf(stderr, "\n");
+ return 1;
+}
+
+int main(int argc, char *argv[])
+{
+ int64_t N;
+ int dist, std_dev, c, size_l, size_r, is_hap = 0;
+ FILE *fpout1, *fpout2;
+ int seed = -1;
+
+ N = 1000000; dist = 500; std_dev = 50;
+ size_l = size_r = 70;
+ while ((c = getopt(argc, argv, "e:d:s:N:1:2:r:R:hX:S:A:")) >= 0) {
+ switch (c) {
+ case 'd': dist = atoi(optarg); break;
+ case 's': std_dev = atoi(optarg); break;
+ case 'N': N = atoi(optarg); break;
+ case '1': size_l = atoi(optarg); break;
+ case '2': size_r = atoi(optarg); break;
+ case 'e': ERR_RATE = atof(optarg); break;
+ case 'r': MUT_RATE = atof(optarg); break;
+ case 'R': INDEL_FRAC = atof(optarg); break;
+ case 'X': INDEL_EXTEND = atof(optarg); break;
+ case 'A': MAX_N_RATIO = atof(optarg); break;
+ case 'S': seed = atoi(optarg); break;
+ case 'h': is_hap = 1; break;
+ }
+ }
+ if (argc - optind < 3) return simu_usage();
+ fpout1 = fopen(argv[optind+1], "w");
+ fpout2 = fopen(argv[optind+2], "w");
+ if (!fpout1 || !fpout2) {
+ fprintf(stderr, "[wgsim] file open error\n");
+ return 1;
+ }
+ if (seed <= 0) seed = time(0)&0x7fffffff;
+ fprintf(stderr, "[wgsim] seed = %d\n", seed);
+ srand48(seed);
+ wgsim_core(fpout1, fpout2, argv[optind], is_hap, N, dist, std_dev,
size_l, size_r);
+
+ fclose(fpout1); fclose(fpout2);
+ return 0;
+}
diff --git a/wgsim_eval.pl b/wgsim_eval.pl
new file mode 100755
index 0000000..5342333
--- /dev/null
+++ b/wgsim_eval.pl
@@ -0,0 +1,294 @@
+#!/usr/bin/perl -w
+
+# Author: lh3
+
+use strict;
+use warnings;
+use Getopt::Std;
+
+die (qq/
+Usage: wgsim_eval.pl <command> <arguments>
+
+Command: alneval evaluate alignment in the SAM format
+ vareval evaluate variant calls in the pileup format
+ unique keep the top scoring hit in SAM
+ uniqcmp compare two alignments without multiple hits
+\n/) if (@ARGV == 0);
+my $command = shift(@ARGV);
+if ($command eq 'alneval') {
+ &alneval;
+} elsif ($command eq 'vareval') {
+ &vareval;
+} elsif ($command eq 'unique') {
+ &unique;
+} elsif ($command eq 'uniqcmp') {
+ &uniqcmp;
+} else {
+ die("[wgsim_eval] unrecognized command.\n");
+}
+exit;
+
+sub alneval {
+ my %opts = (g=>20);
+ getopts('pag:', \%opts);
+ die(qq/
+Usage: wgsim_eval.pl alneval [options] <in.sam>\n
+Options: -p print wrong alignments
+ -g INT correct if withint INT of the true coordinate
+\n/) if (@ARGV == 0 && -t STDIN);
+ my (@c0, @c1, %fnfp);
+ my ($max_q, $flag) = (0, 0);
+ my $gap = $opts{g};
+ $flag |= 1 if (defined $opts{p});
+ while (<>) {
+ next if (/^\@/);
+ my @t = split("\t");
+ next if (@t < 11);
+ my $line = $_;
+ my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1,
$t[2], $t[3], $t[3]);
+ $max_q = $q if ($q > $max_q);
+ # right coordinate
+ $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
+ --$rght;
+ # correct for clipping
+ my ($left0, $rght0) = ($left, $rght);
+ $left -= $1 if (/^(\d+)[SH]/);
+ $rght += $1 if (/(\d+)[SH]$/);
+ $left0 -= $1 if (/(\d+)[SH]$/);
+ $rght0 += $1 if (/^(\d+)[SH]/);
+ # skip unmapped reads
+ next if (($t[1]&0x4) || $chr eq '*');
+ # parse read name and check
+ if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
+ if ($1 ne $chr) { # different chr
+ $is_correct = 0;
+ } else {
+ if ($t[1] & 0x10) { # reverse
+ $is_correct = 0 if (abs($3 - $rght) >
$gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end
of a reads
+ } else {
+ $is_correct = 0 if (abs($2 - $left) >
$gap && abs($2 - $left0) > $gap);
+ }
+ }
+ } else {
+ warn("[wgsim_eval] read '$t[0]' was not generated by
wgsim?\n");
+ next;
+ }
+ ++$c0[$q];
+ ++$c1[$q] unless ($is_correct);
+ @{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
+ ++$fnfp{$t[4]}[0];
+ ++$fnfp{$t[4]}[1] unless ($is_correct);
+ print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
+ }
+ # print
+ my ($cc0, $cc1) = (0, 0);
+ if (!defined($opts{a})) {
+ for (my $i = $max_q; $i >= 0; --$i) {
+ $c0[$i] = 0 unless (defined $c0[$i]);
+ $c1[$i] = 0 unless (defined $c1[$i]);
+ $cc0 += $c0[$i]; $cc1 += $c1[$i];
+ printf("%.2dx %12d / %-12d %12d %.3e\n", $i, $c1[$i],
$c0[$i], $cc0, $cc1/$cc0) if ($cc0);
+ }
+ } else {
+ for (reverse(sort {$a<=>$b} (keys %fnfp))) {
+ next if ($_ == 0);
+ $cc0 += $fnfp{$_}[0];
+ $cc1 += $fnfp{$_}[1];
+ print join("\t", $_, $cc0, $cc1), "\n";
+ }
+ }
+}
+
+sub vareval {
+ my %opts = (g=>10, Q=>200);
+ getopts('g:p', \%opts);
+ my $skip = $opts{g};
+ die("Usage: wgsim_eval.pl vareval [-g $opts{g}] <wgsim.snp>
<pileup.flt>\n") if (@ARGV < 1);
+
+ my $is_print = defined($opts{p})? 1 : 0;
+
+ my ($fh, %snp, %indel);
+ # read simulated variants
+ open($fh, $ARGV[0]) || die;
+ while (<$fh>) {
+ my @t = split;
+ if (@t != 5 || $t[2] eq '-' || $t[3] eq '-') {
+ $indel{$t[0]}{$t[1]} = 1;
+ } else {
+ $snp{$t[0]}{$t[1]} = $t[3];
+ }
+ }
+ close($fh);
+
+ shift(@ARGV);
+ my (@cnt);
+ for my $i (0 .. 3) {
+ for my $j (0 .. $opts{Q}) {
+ $cnt[$i][$j] = 0;
+ }
+ }
+ while (<>) {
+ my @t = split;
+ my $q = $t[5];
+ next if ($t[2] eq $t[3]);
+ $q = $opts{Q} if ($q > $opts{Q});
+ if ($t[2] eq '*') {
+ my $hit = 0;
+ ++$cnt[2][$q];
+ for my $i ($t[1] - $skip .. $t[1] + $skip) {
+ if (defined $indel{$t[0]}{$i}) {
+ $hit = 1; last;
+ }
+ }
+ ++$cnt[3][$q] if ($hit == 0);
+ print STDERR $_ if ($hit == 0 && $is_print);
+ } else {
+ ++$cnt[0][$q];
+ ++$cnt[1][$q] unless (defined $snp{$t[0]}{$t[1]});
+ print STDERR $_ if (!defined($snp{$t[0]}{$t[1]}) &&
$is_print);
+ }
+ }
+
+ for (my $i = $opts{Q} - 1; $i >= 0; --$i) {
+ $cnt[$_][$i] += $cnt[$_][$i+1] for (0 .. 3);
+ }
+
+ for (my $i = $opts{Q}; $i >= 0; --$i) {
+ print join("\t", $i, $cnt[0][$i], $cnt[1][$i], $cnt[2][$i],
$cnt[3][$i]), "\n";
+ }
+}
+
+sub unique {
+ # -f: parameter to recalute mapping quality
+ # -Q: do not recalculate mapping quality
+ # -a, -b, -q, -r: scoring system
+ my %opts = (f=>250.0, q=>5, r=>2, a=>1, b=>3);
+ getopts('Qf:q:r:a:b:m', \%opts);
+ die(qq/
+Usage: wgsim_eval.pl unique [options] <in.sam>\n
+Options: -Q recompuate mapping quality from multiple hits
+ -f FLOAT mapQ=FLOAT*(best1-best2)\/best1 [opts{f}]
+ -a INT matching score (when AS tag is absent) [$opts{a}]
+ -q INT gap open penalty [$opts{q}]
+ -r INT gap extension penalty [$opts{r}]
+\n/) if (@ARGV == 0 && -t STDIN);
+ my $last = '';
+ my $recal_Q = defined($opts{Q});
+ my $multi_only = defined($opts{m});
+ my @a;
+ while (<>) {
+ my $score = -1;
+ print $_ if (/^\@/);
+ $score = $1 if (/AS:i:(\d+)/);
+ my @t = split("\t");
+ next if (@t < 11);
+ if ($score < 0) { # AS tag is unavailable
+ my $cigar = $t[5];
+ my ($mm, $go, $ge) = (0, 0, 0);
+ $cigar =~ s/(\d+)[ID]/++$go,$ge+=$1/eg;
+ $cigar = $t[5];
+ $cigar =~ s/(\d+)M/$mm+=$1/eg;
+ $score = $mm * $opts{a} - $go * $opts{q} - $ge *
$opts{r}; # no mismatches...
+ }
+ $score = 1 if ($score < 1);
+ if ($t[0] ne $last) {
+ &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if
(@a);
+ $last = $t[0];
+ }
+ push(@a, [$score, \@t]);
+ }
+ &unique_aux(\@a, $opts{f}, $recal_Q, $multi_only) if (@a);
+}
+
+sub unique_aux {
+ my ($a, $fac, $is_recal, $multi_only) = @_;
+ my ($max, $max2, $max_i) = (0, 0, -1);
+ for (my $i = 0; $i < @$a; ++$i) {
+ if ($a->[$i][0] > $max) {
+ $max2 = $max; $max = $a->[$i][0]; $max_i = $i;
+ } elsif ($a->[$i][0] > $max2) {
+ $max2 = $a->[$i][0];
+ }
+ }
+ if ($is_recal) {
+ if (!$multi_only || @$a > 1) {
+ my $q = int($fac * ($max - $max2) / $max + .499);
+ $q = 250 if ($q > 250);
+ $a->[$max_i][1][4] = $q < 250? $q : 250;
+ }
+ }
+ print join("\t", @{$a->[$max_i][1]});
+ @$a = ();
+}
+
+sub uniqcmp {
+ my %opts = (q=>20, s=>100, b=>4);
+ getopts('pq:s:b:', \%opts);
+ die(qq/
+Usage: wgsim_eval.pl uniqcmp [options] <in1.sam> <in2.sam>\n
+Options: -q INT confident mapping if mapping quality above INT [$opts{q}]
+ -s INT same mapping if the distance below INT [$opts{s}]
+ -b INT penalty for a difference [$opts{b}]
+\n/) if (@ARGV < 2);
+ my ($fh, %a);
+ warn("[uniqcmp] read the first file...\n");
+ &uniqcmp_aux($ARGV[0], \%a, 0, $opts{b});
+ warn("[uniqcmp] read the second file...\n");
+ &uniqcmp_aux($ARGV[1], \%a, 1, $opts{b});
+ warn("[uniqcmp] stats...\n");
+ my @cnt;
+ $cnt[$_] = 0 for (0..9);
+ for my $x (keys %a) {
+ my $p = $a{$x};
+ my $z;
+ if (defined($p->[0]) && defined($p->[1])) {
+ $z = ($p->[0][0] == $p->[1][0] && $p->[0][1] eq $p->[1][1] &&
abs($p->[0][2] - $p->[1][2]) < $opts{s})? 0 : 1;
+ if ($p->[0][3] >= $opts{q} && $p->[1][3] >= $opts{q}) {
+ ++$cnt[$z*3+0];
+ } elsif ($p->[0][3] >= $opts{q}) {
+ ++$cnt[$z*3+1];
+ } elsif ($p->[1][3] >= $opts{q}) {
+ ++$cnt[$z*3+2];
+ }
+ print STDERR
"$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
+ $p->[0][5]-$p->[1][5], "\n" if ($z && defined($opts{p}) &&
($p->[0][3] >= $opts{q} || $p->[1][3] >= $opts{q}));
+ } elsif (defined($p->[0])) {
+ ++$cnt[$p->[0][3]>=$opts{q}? 6 : 7];
+ print STDERR
"$x\t$p->[0][1]:$p->[0][2]\t$p->[0][3]\t$p->[0][4]\t*\t0\t*\t",
+ $p->[0][5], "\n" if (defined($opts{p}) && $p->[0][3] >=
$opts{q});
+ } else {
+ print STDERR
"$x\t*\t0\t*\t$p->[1][1]:$p->[1][2]\t$p->[1][3]\t$p->[1][4]\t",
+ -$p->[1][5], "\n" if (defined($opts{p}) && $p->[1][3] >=
$opts{q});
+ ++$cnt[$p->[1][3]>=$opts{q}? 8 : 9];
+ }
+ }
+ print "Consistent (high, high): $cnt[0]\n";
+ print "Consistent (high, low ): $cnt[1]\n";
+ print "Consistent (low , high): $cnt[2]\n";
+ print "Inconsistent (high, high): $cnt[3]\n";
+ print "Inconsistent (high, low ): $cnt[4]\n";
+ print "Inconsistent (low , high): $cnt[5]\n";
+ print "Second missing (high): $cnt[6]\n";
+ print "Second missing (low ): $cnt[7]\n";
+ print "First missing (high): $cnt[8]\n";
+ print "First missing (low ): $cnt[9]\n";
+}
+
+sub uniqcmp_aux {
+ my ($fn, $a, $which, $b) = @_;
+ my $fh;
+ $fn = "samtools view $fn |" if ($fn =~ /\.bam/);
+ open($fh, $fn) || die;
+ while (<$fh>) {
+ my @t = split;
+ next if (@t < 11);
+# my $l = ($t[5] =~ /^(\d+)S/)? $1 : 0;
+ my $l = 0;
+ my ($x, $nm) = (0, 0);
+ $nm = $1 if (/NM:i:(\d+)/);
+ $_ = $t[5];
+ s/(\d+)[MI]/$x+=$1/eg;
+ @{$a->{$t[0]}[$which]} = (($t[1]&0x10)? 1 : 0, $t[2], $t[3]-$l, $t[4],
"$x:$nm", $x - $b * $nm);
+ }
+ close($fh);
+}
--
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