/********************************************************************
* I/O functions
* Author: Ge Tan
*******************************************************************/
#include "CNEr.h"
/* --- .Call ENTRY POINT --- */
SEXP myReadBed(SEXP filepath){
// load a filter file into R, and to be a GRanges in 1-based coordinates
filepath = AS_CHARACTER(filepath);
if(!IS_CHARACTER(filepath) || LENGTH(filepath) != 1)
error("'filepath' must be a single string");
if(STRING_ELT(filepath, 0) == NA_STRING)
error("'filepath' is NA");
char *filepath_elt =
R_alloc(strlen(CHAR(STRING_ELT(filepath, 0))) + 1, sizeof(char));
strcpy(filepath_elt, CHAR(STRING_ELT(filepath, 0)));
Rprintf("Reading %s \n", filepath_elt);
struct lineFile *lf = lineFileOpen(filepath_elt, TRUE);
char *row[3];
int nRanges = 0;
while(lineFileRow(lf, row)){
if(sameString(row[0], "track") || sameString(row[0], "browser")) continue;
nRanges++;
}
lineFileClose(&lf);
SEXP chromNames, starts, ends, returnList;
PROTECT(returnList = NEW_LIST(3));
chromNames = NEW_CHARACTER(nRanges);
SET_VECTOR_ELT(returnList, 0, chromNames);
starts = NEW_INTEGER(nRanges);
SET_VECTOR_ELT(returnList, 1, starts);
ends = NEW_INTEGER(nRanges);
SET_VECTOR_ELT(returnList, 2, ends);
int *p_starts, *p_ends;
int j = 0;
p_starts = INTEGER_POINTER(starts);
p_ends = INTEGER_POINTER(ends);
lf = lineFileOpen(filepath_elt, TRUE);
while(lineFileRow(lf, row)){
if(sameString(row[0], "track") || sameString(row[0], "browser")) continue;
p_starts[j] = lineFileNeedNum(lf, row, 1) + 1;
p_ends[j] = lineFileNeedNum(lf, row, 2);
if(p_starts[j] > p_ends[j])
errAbort("start after end line %d of %s", lf->lineIx, lf->fileName);
SET_STRING_ELT(chromNames, j, mkChar(row[0]));
j++;
}
lineFileClose(&lf);
UNPROTECT(1);
return(returnList);
}
/* --- .Call ENTRY POINT --- */
SEXP axt_info(SEXP filepath){
// read a axt file and get the alignment length
filepath = AS_CHARACTER(filepath);
int nrAxtFiles, i;
nrAxtFiles = GET_LENGTH(filepath);
Rprintf("The number of axt files %d\n", nrAxtFiles);
struct axt *curAxt;
struct lineFile *lf;
IntAE *width_buf;
width_buf = new_IntAE(0, 0, 0);
char *filepath_elt;
for(i = 0; i < nrAxtFiles; i++){
R_CheckUserInterrupt();
filepath_elt =
(char *) R_alloc(strlen(CHAR(STRING_ELT(filepath, i)))+1, sizeof(char));
strcpy(filepath_elt, CHAR(STRING_ELT(filepath, i)));
lf = lineFileOpen(filepath_elt, TRUE);
while((curAxt = axtRead(lf)) != NULL){
IntAE_insert_at(width_buf, IntAE_get_nelt(width_buf), curAxt->symCount);
axtFree(&curAxt);
}
lineFileClose(&lf);
}
SEXP width;
PROTECT(width = new_INTEGER_from_IntAE(width_buf));
Rprintf("The number of axt alignments is %d\n", GET_LENGTH(width));
UNPROTECT(1);
return(width);
}
/* --- .Call ENTRY POINT --- */
SEXP myReadAxt(SEXP filepath){
// load a axt file into R, and to be axt object
// This is tested and without memory leak!
// The jim kent's axt struct holds the starts in 0-based.
// Here we put it into 1-based.
filepath = AS_CHARACTER(filepath);
int nrAxtFiles, i, nrAxts;
nrAxtFiles = GET_LENGTH(filepath);
struct axt *axt=NULL, *curAxt;
struct lineFile *lf;
SEXP ans_qSym, ans_tSym, width;
SEXP qNames, qStart, qEnd, qStrand, tNames,
tStart, tEnd, tStrand, score, symCount, returnList;
PROTECT(returnList = NEW_LIST(12));
PROTECT(width = axt_info(filepath));
nrAxts = GET_LENGTH(width);
tNames = NEW_CHARACTER(nrAxts);
SET_VECTOR_ELT(returnList, 0, tNames);
tStart = NEW_INTEGER(nrAxts);
SET_VECTOR_ELT(returnList, 1, tStart);
tEnd = NEW_INTEGER(nrAxts);
SET_VECTOR_ELT(returnList, 2, tEnd);
tStrand = NEW_CHARACTER(nrAxts);
SET_VECTOR_ELT(returnList, 3, tStrand);
//ans_tSym = alloc_XRawList("BStringSet", "BString", width);
ans_tSym = NEW_CHARACTER(nrAxts);
SET_VECTOR_ELT(returnList, 4, ans_tSym);
qNames = NEW_CHARACTER(nrAxts);
SET_VECTOR_ELT(returnList, 5, qNames);
qStart = NEW_INTEGER(nrAxts);
SET_VECTOR_ELT(returnList, 6, qStart);
qEnd = NEW_INTEGER(nrAxts);
SET_VECTOR_ELT(returnList, 7, qEnd);
qStrand = NEW_CHARACTER(nrAxts);
SET_VECTOR_ELT(returnList, 8, qStrand);
// ans_qSym = alloc_XRawList("BStringSet", "BString", width);
ans_qSym = NEW_CHARACTER(nrAxts);
SET_VECTOR_ELT(returnList, 9, ans_qSym);
score = NEW_INTEGER(nrAxts);
SET_VECTOR_ELT(returnList, 10, score);
symCount = NEW_INTEGER(nrAxts);
SET_VECTOR_ELT(returnList, 11, symCount);
UNPROTECT(1);
// cachedXVectorList cached_ans_qSym, cached_ans_tSym;
// cachedCharSeq cached_ans_elt;
// cached_ans_qSym = cache_XVectorList(ans_qSym);
// cached_ans_tSym = cache_XVectorList(ans_tSym);
int *p_qStart, *p_qEnd, *p_tStart, *p_tEnd, *p_score, *p_symCount;
p_qStart = INTEGER_POINTER(qStart);
p_qEnd = INTEGER_POINTER(qEnd);
p_tStart = INTEGER_POINTER(tStart);
p_tEnd = INTEGER_POINTER(tEnd);
p_score = INTEGER_POINTER(score);
p_symCount = INTEGER_POINTER(symCount);
int j = 0;
i = 0;
for(j = 0; j < nrAxtFiles; j++){
R_CheckUserInterrupt();
char *filepath_elt =
(char *) R_alloc(strlen(CHAR(STRING_ELT(filepath, j)))+1, sizeof(char));
strcpy(filepath_elt, CHAR(STRING_ELT(filepath, j)));
lf = lineFileOpen(filepath_elt, TRUE);
while((axt = axtRead(lf)) != NULL){
SET_STRING_ELT(qNames, i, mkChar(axt->qName));
p_qStart[i] = axt->qStart + 1;
p_qEnd[i] = axt->qEnd;
if(axt->qStrand == '+')
SET_STRING_ELT(qStrand, i, mkChar("+"));
else
SET_STRING_ELT(qStrand, i, mkChar("-"));
// cached_ans_elt = get_cachedXRawList_elt(&cached_ans_qSym, i);
// memcpy((char *)
// (&cached_ans_elt)->seq, axt->qSym, axt->symCount * sizeof(char));
SET_STRING_ELT(ans_qSym, i, mkChar(axt->qSym));
SET_STRING_ELT(tNames, i, mkChar(axt->tName));
p_tStart[i] = axt->tStart + 1;
p_tEnd[i] = axt->tEnd;
if(axt->tStrand == '+')
SET_STRING_ELT(tStrand, i, mkChar("+"));
else
SET_STRING_ELT(tStrand, i, mkChar("-"));
// cached_ans_elt = get_cachedXRawList_elt(&cached_ans_tSym, i);
// memcpy((char *)
// (&cached_ans_elt)->seq, axt->tSym, axt->symCount * sizeof(char));
SET_STRING_ELT(ans_tSym, i, mkChar(axt->tSym));
p_score[i] = axt->score;
p_symCount[i] = axt->symCount;
i++;
axtFree(&axt);
}
lineFileClose(&lf);
}
UNPROTECT(1);
//return R_NilValue;
return returnList;
}
