Adds a UCSC 'bin' column

bin.c

/**
 * Author: Pierre Lindenbaum PhD (original source is from Jim Kent: http://genomewiki.ucsc.edu/index.php/Bin_indexing_system
 * Motivation: Adds a UCSC 'bin' column see http://biostar.stackexchange.com/questions/8943/get-rs-number-based-on-position
 * Compilation: gcc bin.c
 * Execute: echo -e "chr1\t10326\t10327\trs112750067" | ./a.out
 * History: updated so it prints all the bins in a at any depth
 */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>


static void binsInRange(
        int chromStart,
        int chromEnd,
        int binId,
        int level,
        int binRowStart,
        int rowIndex,
        int binRowCount,
        int genomicPos,
        int genomicLength,
	int first
        )
        {
	if(first!=1) fputc(',',stdout);
        printf("%d",binId);
        if(level<4)
		{
		int i;
		int childLength=genomicLength/8;
		int childBinRowCount=binRowCount*8;
		int childRowBinStart=binRowStart+binRowCount;
		int firstChildIndex=rowIndex*8;
		int firstChildBin=childRowBinStart+firstChildIndex;
		for(i=0;i< 8;++i)
		        {
		        int childStart=genomicPos+i*childLength;
		        
		        if( chromStart>(childStart+childLength) ||
		                chromEnd<childStart )
		                {
		                continue;
		                }
		        binsInRange(
		                chromStart,
		                chromEnd,
		                firstChildBin+i,
		                level+1,
		                childRowBinStart,
		                firstChildIndex+i,
		                childBinRowCount,
		                childStart,
		                childLength,
				0
		                );
		        }
		}
        }
 


static void bins(int chromStart,int chromEnd)
	{
	int genomicLength=536870912;
	binsInRange(chromStart,chromEnd,0,0,0,0,1,0,genomicLength,1);
	}

static char* readline(FILE* in)
	{
	char* p=NULL;
	int length=0;
	int c;
	while((c=fgetc(in))!=EOF)
		{
		p=realloc(p,(length+2)*sizeof(char));
		if(p==NULL)
			{
			fputs("Out of memory\n",stderr);
			exit(EXIT_FAILURE);
			}
		if(c=='\n')
			{
			p[length]='\0';
			return p;
			}
		p[length]=c;
		p[length+1]='\0';
		length++;	
		}
	return p;
	}

int main(int argc,char** argv)
	{
	char *line;
	while((line=readline(stdin))!=NULL)
		{
		int chromStart=0;
		int chromEnd=0;
                int col=0;
		char *t = strtok(line,"\t");
		while (t != NULL)
		  {
		  switch(col)
			{
			case 0: fputs(t,stdout);break;
			case 1: chromStart=atoi(t);printf("\t%s",t);break;
			case 2: chromEnd=atoi(t);printf("\t%s\t",t);bins(chromStart,chromEnd);break;
			default:printf("\t%s",t);break;
			}
		  t = strtok (NULL, "\t");
		  ++col;
		  }
                fputs("\n",stdout);
		free(line);
		}
	return 0;
	}