mitokmer: kmer_read_m3.cpp annotate

annotate kmer_read_m3.cpp @ 2:a0852bb4b09b draft

planemo upload commit 03463f4b0598df5619def5230de3fb758b4090ba-dirty

author	cstrittmatter
date	Thu, 25 Apr 2019 07:59:05 -0400
parents	1472b4f4fbfe
children

rev	line source
0 1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1 // newkmer_5.cpp load k-mers for all species
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	2 // test reads by SmithWaterman
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	3 // MKM 1 APR 2016
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	4 //-std=c++0x -D__NO_INLINE__ ... at end: -lz
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	5 //#include "stdafx.h"
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	6 #include <fstream>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	7 #include <stdlib.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	8 #include <stdio.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	9 #include <math.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	10 #include <iostream>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	11 #include <sstream>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	12 #include <iomanip>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	13 #include <ostream>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	14 #include <string>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	15 #include <vector>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	16 #include <unordered_set>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	17 #include <time.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	18 //#include <sys/time.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	19 #include <cstddef>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	20 #include <cstring>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	21 #include <algorithm>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	22 #include <set>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	23 #include <zlib.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	24 #include <dirent.h>
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	25 using namespace std;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	26
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	27 const int minalign = 0; //120;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	28 unordered_set<int> myset = { 0};
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	29
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	30 typedef int ptype;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	31 typedef unsigned long long ui64;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	32 typedef unsigned long long ktype;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	33 typedef unsigned int vtype;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	34 typedef unsigned short int otype;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	35 typedef unsigned long long itype;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	36
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	37 const int KSIZE = 30; //kmer size
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	38 const int MAXREP = 2048;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	39 const int REPSHIFT = 11; //(log of maxrep)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	40 const int SAVENUM = 12; //save this many reads
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	41 const itype MAXHASH = (1 << 30); //pow2 size of hashtable
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	42 const int MAXREPROBE = 16;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	43 const int GAPO = 11;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	44 const int GAPX = 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	45 const int MATCH = 5;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	46 const int MISMATCH = -4;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	47 const bool INIGAPPEN = false;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	48 const int MAXALIGN = 1024;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	49 const int beam = 8;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	50
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	51 vector<string> accession;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	52 vector<int> targno;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	53 int mcount, savepos, tct, num_orgs=0, save_target=0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	54 vector<int> gcount, ucount;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	55 ofstream outread;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	56 set<ktype> kmer_seen;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	57 string fdir = ""; //directory for fasta.gz files
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	58
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	59 const char bases[4] = { 'A', 'C', 'G', 'T' };
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	60 const ui64 one = 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	61 const ui64 two = 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	62 const ui64 three = 3;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	63 const ui64 mask = (one << (KSIZE * 2)) - 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	64 const ui64 hiC = one << (KSIZE - 1) * 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	65 const ui64 hiG = two << (KSIZE - 1) * 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	66 const ui64 hiT = three << (KSIZE - 1) * 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	67 const ui64 hi1 = one << 62;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	68 const ui64 hi2 = two << 62;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	69 const ui64 hi3 = three << 62;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	70 const ui64 himask = hi1 - one;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	71
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	72 const unsigned BUFLEN = 0x4000;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	73
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	74 void error(const char* const msg)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	75 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	76 cerr << msg << "\n";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	77 exit(255);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	78 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	79
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	80 string int2str(ktype key)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	81 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	82 string sequence = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	83 for (int i = 0; i < KSIZE; ++i)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	84 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	85 sequence = bases[key & 3] + sequence;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	86 key >>= 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	87 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	88 return sequence;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	89 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	90
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	91 class Tree1
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	92 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	93 public:
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	94
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	95 vector<vector<int>> children;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	96 vector<int> parent;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	97 int root;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	98
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	99 Tree1(int nt)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	100 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	101 vector<int> blank;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	102 root = 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	103 for (int i = 0; i < nt; i++)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	104 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	105 parent.push_back(root);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	106 children.push_back(blank);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	107 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	108 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	109
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	110 ~Tree1()
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	111 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	112 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	113
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	114 void add_edge(int x, int y)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	115 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	116 parent[y] = x;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	117 children[x].push_back(y);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	118 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	119
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	120 int msca(int x, int y)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	121 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	122 //return most specific common ancestor of nodes x and y
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	123 set<int> ancestors;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	124 int z;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	125
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	126 ancestors.insert(root);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	127 z = x;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	128 //cout << x << " " << y << " " << z << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	129 while (z != root)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	130 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	131 ancestors.insert(z);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	132 z = get_parent(z);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	133 //cout << x << " " << y << " " << z << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	134 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	135 z = y;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	136 if (ancestors.find(y) != ancestors.end())
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	137 return x; //x is descendent of y
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	138 while (ancestors.find(z) == ancestors.end())
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	139 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	140 z = get_parent(z);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	141 if (z==x) //y is descendent of x
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	142 return y;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	143 //cout << x << " " << y << " " << z << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	144 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	145 return z; //common ancesctor
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	146 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	147
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	148 int get_parent(int x)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	149 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	150 if (x != root && x > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	151 return parent[x];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	152 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	153 return root;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	154 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	155
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	156 };
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	157
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	158 Tree1 *taxonomy;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	159
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	160 class Hashtable
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	161 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	162 public:
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	163
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	164 itype size;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	165
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	166 struct Cell
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	167 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	168 ktype key;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	169 vtype value;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	170 int org;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	171 ptype position;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	172 bool fstrand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	173 } *pHash;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	174
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	175 Hashtable()
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	176 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	177 size = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	178 pHash = new Cell[MAXHASH];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	179 HashClear();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	180 //for (int i = 1; i<MAXREPROBE; i++)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	181 // reprobeVal[i] = reprobeVal[i - 1] + i; //i*i/2+i/2
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	182 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	183
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	184 ~Hashtable()
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	185 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	186 delete[] pHash;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	187 size = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	188 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	189
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	190 // from code.google.com/p/smhasher/wiki/MurmurHash3
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	191 itype integerHash(ui64 k)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	192 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	193 k ^= k >> 33;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	194 k *= 0xff51afd7ed558ccd;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	195 k ^= k >> 33;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	196 k *= 0xc4ceb9fe1a85ec53;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	197 k ^= k >> 33;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	198 return (itype) k;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	199 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	200
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	201 void HashClear()
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	202 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	203 memset(pHash, 0, MAXHASH * sizeof(Cell));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	204 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	205
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	206 int getHash(ktype key, otype &org, ptype &position, bool &fstrand)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	207 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	208 //0 target=bad
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	209 //returns target if probe present in table
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	210 //sets position and fstrand
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	211 itype index, reprobe, i, hash;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	212
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	213 position = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	214 hash = integerHash(key);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	215 reprobe = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	216 i = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	217 do
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	218 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	219 index = ((hash + reprobe) & (MAXHASH-1)); //for power of 2 size
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	220 reprobe += ++i;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	221 if (pHash[index].value == 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	222 { //empty cell
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	223 return 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	224 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	225 else if (pHash[index].key == key)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	226 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	227 position = pHash[index].position;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	228 fstrand = pHash[index].fstrand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	229 org = pHash[index].org;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	230 return (pHash[index].value);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	231 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	232 } while (reprobe < MAXHASH && i < MAXREPROBE);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	233
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	234 return 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	235 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	236
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	237 void add_kmer(ktype key, vtype target, otype org, ptype position, bool fstrand)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	238 { //add kmer to table
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	239 itype index, reprobe, i, hash;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	240 bool notdone=true;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	241
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	242 hash = integerHash(key);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	243 reprobe = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	244 i = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	245 do
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	246 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	247 index = ((hash + reprobe) & (MAXHASH-1)); //for power of 2 size
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	248 reprobe += ++i;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	249
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	250 if (pHash[index].value == 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	251 { //empty cell
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	252 notdone = false;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	253 pHash[index].key = key;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	254 pHash[index].value = target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	255 pHash[index].org = org;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	256 pHash[index].position = position;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	257 pHash[index].fstrand = fstrand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	258 if (++size > MAXHASH - 32)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	259 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	260 cout << "out of memory in table " << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	261 exit(1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	262 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	263 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	264 } while (notdone);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	265 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	266
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	267 }; //class Hashtable
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	268 Hashtable *ht;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	269
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	270 string process_seq(string seq)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	271 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	272 //format nucleotide sequence to all caps ACTG, all else is N
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	273 string seq2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	274 string::iterator it1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	275 char base;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	276
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	277 seq2 = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	278 for (it1 = seq.begin(); it1 != seq.end(); ++it1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	279 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	280 base = *it1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	281 switch (base)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	282 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	283 case 'a':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	284 seq2 += "A";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	285 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	286 case 'c':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	287 seq2 += "C";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	288 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	289 case 'g':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	290 seq2 += "G";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	291 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	292 case 't':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	293 seq2 += "T";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	294 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	295 case 'A':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	296 seq2 += "A";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	297 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	298 case 'C':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	299 seq2 += "C";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	300 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	301 case 'G':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	302 seq2 += "G";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	303 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	304 case 'T':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	305 seq2 += "T";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	306 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	307 default:
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	308 seq2 += "N";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	309 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	310 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	311 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	312
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	313 return seq2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	314 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	315
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	316 string load_data3(gzFile in)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	317 { //read gzip fasta file and extract nt sequence
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	318 char buf[BUFLEN];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	319 char* offset = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	320 string line;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	321 string sequence = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	322
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	323 while (true)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	324 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	325 int err, len = sizeof(buf)-(offset-buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	326 if (len == 0) error("Buffer to small for input line lengths");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	327
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	328 len = gzread(in, offset, len);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	329
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	330 if (len == 0) break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	331 if (len < 0) error(gzerror(in, &err));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	332
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	333 char* cur = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	334 char* end = offset+len;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	335
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	336 for (char* eol; (cur<end) && (eol = find(cur, end, '\n')) < end; cur = eol + 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	337 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	338 line = string(cur, eol);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	339 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	340 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	341 if (line.length() > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	342 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	343 if (line.at(0) == '>')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	344 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	345 sequence += "N"; //contig separator
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	346 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	347 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	348 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	349 sequence += process_seq(line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	350 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	351 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	352 //cout << line << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	353 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	354
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	355 // any trailing data in [eol, end) now is a partial line
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	356 offset = copy(cur, end, buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	357 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	358
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	359 // trailing data without eol
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	360 line = string(buf, offset);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	361 if (gzclose(in) != Z_OK) error("failed gzclose");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	362
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	363 return sequence;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	364 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	365
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	366 int tableM, tableI, *tableD;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	367
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	368 void tableinit()
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	369 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	370 int i,j;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	371 const int NINF = -2000000000;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	372
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	373 tableM[0] = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	374 tableI[0] = NINF;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	375 tableD[0] = NINF;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	376 for (i = 1; i<MAXALIGN; i++) //initialize upper row
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	377 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	378 j = (0 > i - beam - 1) ? 0 : i - beam - 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	379 tableI[j*MAXALIGN + i] = NINF;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	380 if (INIGAPPEN)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	381 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	382 tableD[jMAXALIGN + i] = -GAPO - (i - 1)GAPX;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	383 tableM[jMAXALIGN + i] = -GAPO - (i - 1)GAPX;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	384 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	385 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	386 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	387 tableD[0 + i] = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	388 tableM[0 + i] = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	389 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	390 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	391 for (j = 1; j<MAXALIGN; j++) //init left column
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	392 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	393 i = (0 > j - beam - 1) ? 0 : j - beam - 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	394 tableD[j*MAXALIGN + i] = NINF;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	395 if (INIGAPPEN)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	396 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	397 tableI[jMAXALIGN + i] = -GAPO - (j - 1)GAPX;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	398 tableM[jMAXALIGN + i] = -GAPO - (j - 1)GAPX;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	399 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	400 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	401 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	402 tableI[j*MAXALIGN + i] = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	403 tableM[j*MAXALIGN + i] = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	404 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	405 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	406 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	407
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	408 int align(string dna1, string dna2)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	409 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	410 //smith waterman alignment with beam
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	411 //returns alignment score
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	412 int b1, b2, len1, len2, tindex;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	413 int b,bb,c,cc;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	414 int i, j, maxval, startx, starty;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	415 int i1, i2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	416
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	417 len1 = dna1.length() + 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	418 len2 = dna2.length() + 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	419
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	420 j=1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	421 do
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	422 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	423 i = (j <= beam) ? j : j - beam;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	424 i2 = (j + beam > len1) ? len1 : j + beam;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	425 do
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	426 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	427 maxval = max(max(tableM[(j-1)MAXALIGN + i-1], tableI[(j-1)MAXALIGN + i-1]), tableD[(j-1)*MAXALIGN + i-1]);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	428 //copy/replace
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	429 if (dna1[i-1] != dna2[j-1])
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	430 maxval += MISMATCH;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	431 else maxval += MATCH;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	432 tableM[j*MAXALIGN + i] = maxval;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	433
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	434 b=tableM[(j-1)*MAXALIGN + i] - GAPO; //new gap
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	435 bb = tableI[(j-1)*MAXALIGN + i] -GAPX; //extend
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	436 tableI[j*MAXALIGN + i] = (bb<b) ? b : bb;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	437
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	438 c=tableM[j*MAXALIGN + i-1] - GAPO; //new gap
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	439 cc = tableD[j*MAXALIGN + i-1] -GAPX; //extend
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	440 tableD[j*MAXALIGN + i] = (cc<c) ? c : cc;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	441 } while(++i < i2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	442 } while(++j < len2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	443
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	444 i = len1 - 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	445 j = len2 - 1; //process last entry
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	446
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	447 maxval = max(max(tableM[jMAXALIGN + i], tableI[jMAXALIGN + i]), tableD[j*MAXALIGN + i]);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	448
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	449 return maxval;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	450
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	451 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	452
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	453 int process_read(string &sequence, string acc, int start, int stop)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	454 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	455 //returns id of read, 0 = no match, updates gcount, ucount
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	456 //will do align for first minalign of each target
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	457 //will save first SAVENUM reads of each target
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	458
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	459 char base;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	460 int it1, it2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	461 string kmer, sequence2, dna1, dna1r, dna2, fname, finalkeystr;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	462 ktype keyF, keyR, key;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	463 int i, cpos, minscr, gpos;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	464 bool fstrand1, fstrand2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	465 int readlength = stop - start + 1, readlen2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	466 int st2, scr, stlen2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	467 ktype target, final_targ=0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	468 ptype position;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	469 otype org;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	470 int maxct, totct, rtarg=0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	471 bool reject = false;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	472
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	473 cpos = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	474 keyF = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	475 keyR = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	476 gpos = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	477 minscr = 5 * sequence.length() / 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	478 for (it1 = start; it1 <= stop; ++it1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	479 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	480 base = sequence.at(it1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	481 switch (base)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	482 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	483 case 'A':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	484 keyF = (keyF << 2) & mask;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	485 keyR = (keyR >> 2) \| hiT;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	486 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	487 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	488 case 'C':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	489 keyF = ((keyF << 2) & mask) \| 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	490 keyR = (keyR >> 2) \| hiG;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	491 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	492 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	493 case 'G':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	494 keyF = ((keyF << 2) & mask) \| 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	495 keyR = (keyR >> 2) \| hiC;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	496 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	497 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	498 case 'T':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	499 keyF = ((keyF << 2) & mask) \| 3;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	500 keyR = keyR >> 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	501 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	502 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	503 case 'a':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	504 keyF = (keyF << 2) & mask;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	505 keyR = (keyR >> 2) \| hiT;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	506 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	507 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	508 case 'c':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	509 keyF = ((keyF << 2) & mask) \| 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	510 keyR = (keyR >> 2) \| hiG;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	511 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	512 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	513 case 'g':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	514 keyF = ((keyF << 2) & mask) \| 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	515 keyR = (keyR >> 2) \| hiC;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	516 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	517 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	518 case 't':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	519 keyF = ((keyF << 2) & mask) \| 3;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	520 keyR = keyR >> 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	521 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	522 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	523 default:
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	524 cpos = 0; //ambiguous character
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	525 keyF = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	526 keyR = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	527 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	528 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	529 gpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	530 if (cpos == KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	531 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	532 key = keyF < keyR ? keyF : keyR;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	533 target = ht->getHash(key, org, position, fstrand2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	534 //position is ending base, 1-based
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	535 if (target > 0 && gcount[target] < minalign && target != final_targ)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	536 { //do alignment on initial reads of a species
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	537 fname = fdir + accession[org] + ".fasta.gz";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	538 sequence2 = load_data3(gzopen(fname.c_str(), "rb"));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	539 stlen2 = sequence2.length();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	540 fstrand1 = (keyF < keyR);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	541 readlen2 = readlength;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	542 if (fstrand1 == fstrand2)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	543 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	544 st2 = position - it1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	545 if (st2 < 0) st2 = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	546 if (st2 + readlen2 > stlen2) readlen2 = stlen2 - st2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	547 dna1 = sequence.substr(start, readlength);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	548 dna2 = sequence2.substr(st2, readlen2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	549 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	550 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	551 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	552 //reverse complement dna1
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	553 st2 = position - KSIZE + 2 + it1 - readlength;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	554 if (st2 < 0) st2 = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	555 if (st2 + readlen2 > stlen2) readlen2 = stlen2 - st2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	556 //dna1 = sequence.substr(start, readlength);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	557 dna1 = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	558 for (it2 = stop; it2 >= start; --it2)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	559 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	560 base = sequence.at(it2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	561 switch (base)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	562 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	563 case 'A':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	564 dna1.push_back('T');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	565 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	566 case 'C':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	567 dna1.push_back('G');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	568 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	569 case 'G':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	570 dna1.push_back('C');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	571 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	572 case 'T':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	573 dna1.push_back('A');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	574 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	575 default:
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	576 dna1.push_back('N');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	577 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	578 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	579 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	580 dna2 = sequence2.substr(st2, readlen2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	581 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	582 scr = align(dna1, dna2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	583 if (scr < minscr)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	584 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	585 rtarg = target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	586 target = 0; //fail
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	587 reject = true;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	588 //cout << rtarg << ": failed " << scr << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	589 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	590 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	591 if (final_targ > 0 && target > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	592 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	593 final_targ = taxonomy->msca(target, final_targ);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	594 finalkeystr = int2str(key);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	595 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	596 else if (target > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	597 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	598 final_targ = target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	599 finalkeystr = int2str(key);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	600 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	601 if (target > 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	602 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	603 if (kmer_seen.find(key) == kmer_seen.end())
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	604 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	605 ucount[target]++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	606 kmer_seen.insert(key);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	607 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	608 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	609 cpos--;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	610 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	611 } //it
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	612 /*
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	613 if (final_targ > 1 && gcount[final_targ] < SAVENUM && save_target == 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	614 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	615 outread << ">" << final_targ << ":" << acc << endl << sequence.substr(start, stop-start+1) << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	616 outread << "[" << finalkeystr << "]" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	617 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	618 if (final_targ > 1 && final_targ == save_target)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	619 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	620 outread << ">" << final_targ << ":" << acc << endl << sequence.substr(start, stop-start+1) << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	621 } */
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	622 gcount[final_targ]++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	623 tct++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	624
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	625 return final_targ;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	626 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	627
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	628
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	629 void process_kmer(string sequence, vtype target, otype org, ptype position, bool fstrand)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	630 { //adds kmer from datafile into hashtable
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	631 char base;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	632 string::iterator it1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	633 int cpos, gpos;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	634 ui64 keyF;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	635
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	636 cpos = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	637 gpos = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	638 keyF = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	639
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	640 for (it1 = sequence.begin(); it1 != sequence.end(); ++it1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	641 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	642 base = *it1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	643 switch (base)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	644 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	645 case 'A':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	646 keyF = (keyF << 2) & mask;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	647 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	648 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	649 case 'C':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	650 keyF = ((keyF << 2) & mask) \| 1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	651 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	652 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	653 case 'G':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	654 keyF = ((keyF << 2) & mask) \| 2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	655 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	656 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	657 case 'T':
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	658 keyF = ((keyF << 2) & mask) \| 3;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	659 cpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	660 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	661 default:
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	662 cpos = 0; //ambiguous character
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	663 keyF = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	664 break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	665 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	666 if (cpos == KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	667 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	668 ht->add_kmer(keyF, target, org, position, fstrand);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	669 cpos--;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	670 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	671 gpos++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	672 } //it
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	673
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	674 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	675
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	676 void process_qual(string acc, string &seq, string &qual)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	677 { //uses PHRED 33 scores
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	678 //to trim read and pass it to process_read
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	679 const int cutoff_qual = 17;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	680 const char cutoff_char = 32 + cutoff_qual;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	681 int start, stop, target, i;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	682 int window_size = 4;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	683 int window_val, window_cut = cutoff_qual * window_size;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	684 string trim_seq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	685
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	686 stop = seq.length()-1;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	687 start = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	688 //trim all low qual bases from end
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	689 while (qual.at(start) < cutoff_char && start < stop)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	690 start++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	691 while (qual.at(stop) < cutoff_char && stop > start)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	692 stop--;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	693 //trim by window
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	694 if (start < stop - window_size)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	695 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	696 window_val = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	697 for (i=0; i<window_size; i++)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	698 window_val += qual.at(start+i) - 32;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	699 while (window_val < window_cut && start < stop - window_size)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	700 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	701 window_val += qual.at(start+window_size) - qual.at(start);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	702 start++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	703 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	704 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	705 if (start < stop - window_size)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	706 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	707 window_val = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	708 for (i=0; i<window_size; i++)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	709 window_val += qual.at(stop-i) - 32;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	710 while (window_val < window_cut && start < stop - window_size)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	711 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	712 window_val += qual.at(stop-window_size) - qual.at(stop);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	713 stop--;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	714 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	715 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	716 //trim_seq = seq.substr(start,stop-start+1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	717 if (stop - start >= KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	718 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	719 target = process_read(seq,acc,start,stop);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	720 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	721
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	722 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	723
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	724 void process_fqgz(gzFile in)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	725 { //read gzip fastq file and extract sequence and quality lines
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	726 //passes them to process_qual
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	727 char buf[BUFLEN];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	728 char* offset = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	729 string line, seq, acc;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	730 int mod4=0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	731
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	732 while (true)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	733 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	734 int err, len = sizeof(buf)-(offset-buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	735 if (len == 0) error("Buffer to small for input line lengths");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	736
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	737 len = gzread(in, offset, len);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	738
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	739 if (len == 0) break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	740 if (len < 0) error(gzerror(in, &err));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	741
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	742 char* cur = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	743 char* end = offset+len;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	744
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	745 for (char* eol; (cur<end) && (eol = find(cur, end, '\n')) < end; cur = eol + 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	746 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	747 line = string(cur, eol);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	748 if (line.back() == '\r') //windows
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	749 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	750 if (line.length() > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	751 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	752 if (mod4 == 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	753 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	754 seq = line;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	755 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	756 else if (mod4 == 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	757 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	758 acc = line;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	759 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	760 else if (mod4 == 3)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	761 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	762 process_qual(acc, seq, line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	763 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	764 mod4 = (mod4 + 1) % 4;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	765
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	766 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	767 //cout << line << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	768 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	769
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	770 // any trailing data in [eol, end) now is a partial line
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	771 offset = copy(cur, end, buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	772 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	773
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	774 // trailing data without eol
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	775 line = string(buf, offset);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	776
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	777 if (gzclose(in) != Z_OK) error("failed gzclose");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	778 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	779
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	780 void process_fagz(gzFile in)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	781 { //read gzip fasta file and extract sequence
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	782 //passes read to process_read
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	783 char buf[BUFLEN];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	784 char* offset = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	785 string line;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	786 string sequence = "", acc = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	787 int c1, c2, target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	788
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	789 cout << "true" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	790
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	791 while (true)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	792 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	793 int err, len = sizeof(buf)-(offset-buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	794 if (len == 0) error("Buffer to small for input line lengths");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	795
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	796 len = gzread(in, offset, len);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	797
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	798 if (len == 0) break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	799 if (len < 0) error(gzerror(in, &err));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	800
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	801 char* cur = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	802 char* end = offset+len;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	803
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	804 for (char* eol; (cur<end) && (eol = find(cur, end, '\n')) < end; cur = eol + 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	805 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	806 line = string(cur, eol);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	807 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	808 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	809 if (line.length() > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	810 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	811 if (line.at(0) == '>')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	812 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	813 if (sequence.length() > KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	814 { // process previous sequence
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	815 target = process_read(sequence, acc, 0, sequence.length()-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	816 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	817 sequence = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	818 acc = line.substr(1,line.length()-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	819 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	820 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	821 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	822 sequence += line;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	823 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	824 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	825 //cout << line << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	826 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	827
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	828 // any trailing data in [eol, end) now is a partial line
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	829 offset = copy(cur, end, buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	830 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	831 if (sequence.length() > KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	832 { //last one
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	833 target = process_read(sequence, acc, 0, sequence.length()-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	834 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	835 // trailing data without eol
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	836 line = string(buf, offset);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	837 if (gzclose(in) != Z_OK) error("failed gzclose");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	838
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	839 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	840
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	841 int process_gzkmers(gzFile in)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	842 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	843
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	844 char buf[BUFLEN];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	845 char* offset = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	846 string line;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	847 int target, count, org, position, tct=0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	848 string sequence;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	849 char strand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	850 bool fstrand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	851
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	852 while (true)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	853 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	854 int err, len = sizeof(buf)-(offset-buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	855 if (len == 0) error("Buffer to small for input line lengths");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	856
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	857 len = gzread(in, offset, len);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	858
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	859 if (len == 0) break;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	860 if (len < 0) error(gzerror(in, &err));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	861
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	862 char* cur = buf;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	863 char* end = offset+len;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	864
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	865 for (char* eol; (cur<end) && (eol = find(cur, end, '\n')) < end; cur = eol + 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	866 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	867 line = string(cur, eol);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	868 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	869 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	870 if (line.length() > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	871 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	872 replace(line.begin(), line.end(), ',', ' ');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	873 istringstream ss(line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	874 if (ss >> sequence >> target >> org >> position >> strand >> count)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	875 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	876 fstrand = (strand == 'F');
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	877 process_kmer(sequence, target, org, position, fstrand);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	878 tct++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	879 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	880 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	881 //cout << line << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	882 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	883
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	884 // any trailing data in [eol, end) now is a partial line
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	885 offset = copy(cur, end, buf);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	886 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	887 // trailing data without eol
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	888 line = string(buf, offset);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	889 if (gzclose(in) != Z_OK) error("failed gzclose");
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	890
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	891 return tct;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	892
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	893 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	894
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	895 void process_fq(string rname)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	896 { //read fastq file and extract sequence and quality lines
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	897 //passes them to process_qual
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	898 string line, seq, acc= "", lseq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	899 ifstream fin;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	900 int target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	901 int mod4=0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	902
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	903 fin.open(rname);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	904 if (fin)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	905 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	906 while (getline(fin, line))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	907 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	908 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	909 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	910 stringstream linestream(line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	911 linestream >> lseq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	912 if (lseq.length() > 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	913 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	914 if (mod4 == 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	915 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	916 seq = lseq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	917 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	918 else if (mod4 == 0)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	919 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	920 acc = lseq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	921 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	922 else if (mod4 == 3)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	923 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	924 process_qual(acc, seq, lseq);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	925 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	926 mod4 = (mod4 + 1) % 4;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	927 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	928 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	929 fin.close();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	930 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	931 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	932
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	933 void process_fa(string rname)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	934 { //read unzipped fasta file and extract sequence
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	935 //passes read to process_read
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	936 string sequence = "", line, lseq, acc= "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	937 ifstream fin;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	938 int target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	939
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	940 fin.open(rname);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	941 if (fin)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	942 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	943 while (getline(fin, line))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	944 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	945 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	946 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	947 stringstream linestream(line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	948 linestream >> lseq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	949 if (lseq[0] == '>')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	950 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	951 if (sequence.length() > KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	952 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	953 target = process_read(sequence, acc, 0, sequence.length()-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	954 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	955 sequence = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	956 acc = lseq.substr(1,lseq.length()-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	957 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	958 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	959 sequence += lseq;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	960 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	961 fin.close();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	962 if (sequence.length() > KSIZE)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	963 { //last one
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	964 target = process_read(sequence, acc, 0, sequence.length()-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	965 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	966 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	967 else
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	968 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	969 cout << "nark " << rname << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	970 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	971 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	972
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	973 int main(int argc, char* argv[])
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	974 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	975 int i,j,num_jobs;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	976 vtype target;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	977 ptype position;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	978 char strand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	979 bool fstrand;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	980 string header, jstr, fname, line, r1name, r2name = "", oname1, oname2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	981 int refi, targi, strni, count, org, num_targ;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	982 ifstream fin;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	983 string genus, species, acc, sequence, lseq, remainder;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	984 vector<vector<string>> fnames;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	985 vector<string> jnames;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	986 vector<int> jcounts;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	987 vector<string>::iterator it2;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	988 string trname, s1, s2, s3,s4;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	989 string argst, wdir = "", dname = "", jname = "", jfile = "", jdir = "";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	990 string iname = "mitochondria_data.txt"; //text file of groups for probe design
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	991 string tname = "mitochondria_tree.txt"; //edges in taxonomy tree
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	992 string pname = "mitochondria_probes.txt.gz";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	993 if (argc > 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	994 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	995 for (i = 1; i < argc; i++)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	996 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	997 argst = argv[i];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	998 if (argst == "-wdir")
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	999 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1000 wdir = argv[i+1];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1001 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1002 if (argst == "-f1")
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1003 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1004 r1name =argv[i+1];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1005 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1006 if (argst == "-f2")
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1007 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1008 r2name =argv[i+1];
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1009 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1010 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1011 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1012 iname = wdir + iname;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1013 tname = wdir + tname;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1014 pname = wdir + pname;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1015
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1016 ht = new Hashtable();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1017 //load strain list
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1018
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1019
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1020 cout << "r1 " << r1name << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1021 cout << "r2 " << r2name << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1022 cout << "wd " << wdir << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1023 fin.open(iname);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1024 if (fin)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1025 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1026 while (getline(fin, line))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1027 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1028 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1029 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1030 if (line.length() > 1)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1031 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1032 stringstream linestream(line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1033 linestream >> targi >> acc;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1034 accession.push_back(acc);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1035 targno.push_back(targi);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1036 if (targi > num_targ)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1037 num_targ = targi;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1038 num_orgs++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1039 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1040 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1041 fin.close();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1042 cout << num_orgs << " strains" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1043 num_targ++;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1044 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1045 taxonomy = new Tree1(num_targ);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1046
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1047 //load taxonomy tree
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1048 fin.open(tname);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1049 if (fin)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1050 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1051 while (getline(fin, line))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1052 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1053 if (line.back() == '\r')
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1054 line.pop_back();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1055 stringstream linestream(line);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1056 linestream >> i >> j;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1057 taxonomy->add_edge(i,j);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1058 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1059 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1060 else exit(1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1061 fin.close();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1062 cout << "tree loaded" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1063
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1064 //load kmer database
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1065 tct = process_gzkmers(gzopen(pname.c_str(), "rb"));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1066 cout << tct << " kmers loaded" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1067 if (tct < 2) exit(1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1068
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1069 //process reads
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1070 gcount.resize(num_targ,0);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1071 ucount.resize(num_targ,0);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1072 fill(gcount.begin(), gcount.end(), 0);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1073 fill(ucount.begin(), ucount.end(), 0);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1074 kmer_seen.clear();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1075 tct = 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1076 s1 = ".fastq.gz";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1077 s2 = ".fasta";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1078 s3 = ".fastq";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1079 s4 = ".fasta.gz";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1080 int slen = r1name.length();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1081 char sch = r1name.at(slen-1);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1082 cout << slen << " : " << sch << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1083 if (equal(s1.rbegin(), s1.rend(), r1name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1084 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1085 process_fqgz(gzopen(r1name.c_str(), "rb"));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1086 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1087 else if (equal(s2.rbegin(), s2.rend(), r1name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1088 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1089 process_fa(r1name.c_str());
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1090 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1091 else if (equal(s3.rbegin(), s3.rend(), r1name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1092 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1093 process_fq(r1name.c_str());
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1094 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1095 else if (equal(s4.rbegin(), s4.rend(), r1name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1096 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1097 process_fagz(gzopen(r1name.c_str(), "rb"));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1098 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1099 cout << tct << " reads loaded" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1100 if (r2name.length() > 1 && r2name != "none")
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1101 { //second file?
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1102 if (equal(s1.rbegin(), s1.rend(), r2name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1103 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1104 process_fqgz(gzopen(r2name.c_str(), "rb"));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1105 cout << tct << " reads loaded" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1106 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1107 else if (equal(s2.rbegin(), s2.rend(), r2name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1108 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1109 process_fa(r2name.c_str());
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1110 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1111 else if (equal(s3.rbegin(), s3.rend(), r2name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1112 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1113 process_fq(r2name.c_str());
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1114 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1115 else if (equal(s4.rbegin(), s4.rend(), r2name.rbegin()))
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1116 {
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1117 process_fagz(gzopen(r2name.c_str(), "rb"));
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1118 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1119 cout << tct << " reads loaded" << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1120 }
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1121
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1122 oname2 = wdir + "result.txt";
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1123 ofstream out2(oname2);
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1124 for (i=0; i<num_targ; i++)
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1125 out2 << i << "," << gcount[i] << "," << ucount[i] << endl;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1126 out2.close();
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1127
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1128 delete taxonomy;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1129 delete ht;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1130
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1131 return 0;
1472b4f4fbfe planemo upload commit a4aeec0f52695b1cbda85ed1faf85d66ba897ab2 cstrittmatter parents: diff changeset	1132 }

Mercurial > repos > cstrittmatter > mitokmer

annotate kmer_read_m3.cpp @ 2:a0852bb4b09b draft