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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#include <klib/rc.h>
#include <klib/data-buffer.h>
#include <klib/sort.h>
#include "KFileHelper.h"
#include "analysis.h"
#include "Globals.h"
#include <stdlib.h>
#include <string.h>
#include <assert.h>
static rc_t ParseAnalysis(Analysis *rslt, unsigned lines, char *src) {
unsigned i;
rslt->N = lines;
memset(&rslt->line[0], 0, lines * sizeof(rslt->line[0]));
for (i = 0; i != lines; ++i) {
char *endp;
char *tab;
endp = strchr(src, 0);
assert(endp);
rslt->line[i].name = src;
tab = strchr(src, '\t');
if (!tab) break;
src = tab + 1;
tab[0] = '\0';
rslt->line[i].refID = src;
tab = strchr(src, '\t');
if (!tab) break;
src = tab + 1;
tab[0] = '\0';
tab = strchr(src, '\t');
if (!tab) break;
src = tab + 1;
rslt->line[i].bamFile = src;
tab = strchr(src, '\t');
if (!tab) break;
src = tab + 1;
tab[0] = '\0';
rslt->line[i].asoFile = src;
tab = strchr(src, '\t');
if (!tab) break;
tab[0] = '\0';
src = endp + 1;
}
for (i = 0; i != lines; ++i) {
if (rslt->line[i].name == NULL ||
rslt->line[i].refID == NULL ||
rslt->line[i].bamFile == NULL ||
rslt->line[i].asoFile == NULL
)
{
return RC(rcApp, rcFile, rcReading, rcData, rcCorrupt);
}
}
return 0;
}
static int CC CompAnalysisLineBamFile(const void *A, const void *B, void *ignore) {
const AnalysisLine *a = A;
const AnalysisLine *b = B;
int rslt = strcmp(a->bamFile, b->bamFile);
if (rslt == 0)
rslt = strcmp(a->name, b->name);
return rslt;
}
const char *AnalysisNextBAMFile(const char *last) {
unsigned i;
if (last == NULL) {
return G.analysis->line[0].bamFile;
}
for (i = 1; i < G.analysis->N; ++i) {
if (strcmp(last, G.analysis->line[i].bamFile) > 0) {
return G.analysis->line[i].bamFile;
}
}
return NULL;
}
AnalysisLine *AnalysisMatch(const char *bamFile, const char *name) {
unsigned i;
for (i = 0; i != G.analysis->N; ++i) {
if (strcmp(bamFile, G.analysis->line[i].bamFile) == 0 &&
strcmp(name, G.analysis->line[i].name) == 0
)
{
return &G.analysis->line[i];
}
}
return NULL;
}
rc_t LoadAnalysis(const char *fileName) {
rc_t rc;
KDataBuffer buf;
uint64_t lines;
memset(&buf, 0, sizeof(buf));
buf.elem_bits = 8;
rc = LoadFile(&buf, &lines, G.inDir, fileName);
if (rc == 0) {
if (lines > 0 && buf.elem_count > 0) {
G.analysis = malloc(sizeof(*G.analysis) + (lines - 1) * sizeof(G.analysis->line[0]) + buf.elem_count);
if (G.analysis)
memmove(&G.analysis->line[lines], buf.base, buf.elem_count);
else
rc = RC(rcApp, rcFile, rcReading, rcMemory, rcExhausted);
}
else
rc = RC(rcApp, rcFile, rcReading, rcData, rcEmpty);
}
KDataBufferWhack(&buf);
if (rc == 0) {
rc = ParseAnalysis(G.analysis, lines, (char *)&G.analysis->line[lines]);
}
return rc;
}
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