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consensus.c
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consensus.c
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/* makes consensus fasta file from pileup */
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#define TO_NEXT_TAB while (getchar() != '\t')
#define TO_NEXT_NL while (getchar() != '\n')
#define chr_l 30
static char cur_chr[chr_l+1];
static char new_chr[chr_l+1];
static int nwarns = 0, maxwarns = 10;
static inline int char2base(char c)
{
return ((c >> 1) & 0x3);
}
static inline int numberp(char c)
{
return c >= '0' && c <= '9';
}
static int nchars = 0; /* number of bases printed */
void parse_chr()
{
char c;
int i;
for (c = getchar(), i = 0; c != '\t' && i < chr_l; c = getchar(), ++i) {
new_chr[i] = c;
}
new_chr[i] = '\0';
if (c != '\t' && nwarns < maxwarns) {
fprintf(stderr, "Warning, chromosome name truncated to %s.\n", new_chr);
nwarns++;
}
ungetc(c, stdin);
if (strcmp(cur_chr, new_chr) != 0){
if (cur_chr[0] != '\0') {
printf("\n");
}
strcpy(cur_chr, new_chr);
printf(">%s\n", cur_chr);
nchars = 0;
}
}
int parse_number()
{
char c;
int number = 0;
for (c = getchar(); numberp(c); c = getchar()) {
number *= 10;
number += c & 0xF;
}
ungetc(c, stdin);
return number;
}
/* statics for parse_pileup_line */
static unsigned char pileup_c;
static int cur_position = 0, new_position;
static char ref_base;
static int nucs[4] = {0};
static char bases[4] = {'A','C','T','G'};
static int dels = 0;
/* just reads over indel and ignores it */
void do_indel()
{
int length = parse_number();
for(; length > 0; --length) {
getchar();
}
}
void do_del()
{
dels++;
}
void do_quality()
{
getchar(); /* read over quality */
}
void do_base()
{
nucs[char2base(pileup_c)]++;
}
void do_dot()
{
if ('N' == ref_base && nwarns < maxwarns) {
fprintf(stderr, "Warning: N ref base and dot\n");
}
else{
nucs[char2base(ref_base)]++;
}
}
void do_comma()
{
if ('N' == ref_base && nwarns < maxwarns) {
fprintf(stderr, "Warning: N ref base and comma\n");
}
else {
nucs[char2base(ref_base)]++;
}
}
void do_tab()
{
TO_NEXT_NL;
ungetc('\n', stdin);
}
void do_nothing()
{
return;
}
void print_base()
{
int i, max = nucs[0], maxidx = 0;
for (i = 1; i < 4; i++) {
if (nucs[i] > max){
max = nucs[i];
maxidx = i;
}
}
if (max > 0){
printf("%c", bases[maxidx]);
}
else{
printf("N");
}
nchars++;
if (nchars >= 80){
printf("\n");
nchars = 0;
}
}
typedef void (*Pfun)(void);
static Pfun fun_table[8] = {do_nothing, /* 0 */
do_indel, /* 1 */
do_del, /* 2 */
do_quality, /* 3 */
do_base, /* 4 */
do_dot, /* 5 */
do_comma, /* 6 */
do_tab}; /* 7 */
static unsigned char a2f[256] = {
/* 0 1 2 3 4 5 6 7 */
/* 8 9 A B C D E F */
0, 0, 0, 0, 0, 0, 0, 0, /* 00 */
0, 7, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, /* 10 */
0, 0, 0, 0, 0, 0, 0, 0,
0,/* */0,/*!*/0,/*"*/0,/*#*/0,/*$*/0,/*%*/0,/*&*/0,/*'*/ /* 20 */
0,/*(*/0,/*)*/2,/***/1,/*+*/6,/*,*/1,/*-*/5,/*.*/0,/*/*/
0,/*0*/0,/*1*/0,/*2*/0,/*3*/0,/*4*/0,/*5*/0,/*6*/0,/*7*/ /* 30 */
0,/*8*/0,/*9*/0,/*:*/0,/*;*/0,/*<*/0,/*=*/0,/*>*/0,/*?*/
0,/*@*/4,/*A*/0,/*B*/4,/*C*/0,/*D*/0,/*E*/0,/*F*/4,/*G*/ /* 40 */
0,/*H*/0,/*I*/0,/*J*/0,/*K*/0,/*L*/0,/*M*/0,/*N*/0,/*O*/
0,/*P*/0,/*Q*/0,/*R*/0,/*S*/4,/*T*/0,/*U*/0,/*V*/0,/*W*/ /* 50 */
0,/*X*/0,/*Y*/0,/*Z*/0,/*[*/0,/*\*/0,/*]*/3,/*^*/0,/*_*/
0,/*`*/4,/*a*/0,/*b*/4,/*c*/0,/*d*/0,/*e*/0,/*f*/4,/*g*/ /* 60 */
0,/*h*/0,/*i*/0,/*j*/0,/*k*/0,/*l*/0,/*m*/0,/*n*/0,/*o*/
0,/*p*/0,/*q*/0,/*r*/0,/*s*/4,/*t*/0,/*u*/0,/*v*/0,/*w*/ /* 70 */
0,/*x*/0,/*y*/0,/*z*/0,/*{*/0,/*|*/0,/*}*/0,/*~*/0
};
void parse_pileup_line()
{
memset(nucs, 0, sizeof(nucs));
dels = 0;
parse_chr();
TO_NEXT_TAB;
new_position = parse_number();
for (; cur_position < new_position - 1; cur_position++) {
printf("N");
nchars++;
if (nchars >= 80) {
printf("\n");
nchars = 0;
}
}
cur_position = new_position;
TO_NEXT_TAB;
ref_base = getchar();
TO_NEXT_TAB;
TO_NEXT_TAB; /* number of pileups */
/* now read main pileup to tab (qualities follow) */
while((pileup_c = getchar()) != '\n') {
fun_table[a2f[pileup_c]]();
}
print_base();
}
void parse_pileup()
{
char nextchar;
int nlines = 0;
while((nextchar = getc(stdin)) != EOF) {
nlines++;
ungetc(nextchar, stdin);
parse_pileup_line();
}
}
int main(int argc, char *argv[])
{
cur_chr[0] = '\0';
new_chr[0] = '\0';
parse_pileup();
printf("\n");
return 0;
}