int main(int argc, char *argv[])
/* Process command line. */
{
if (argc != 4)
errAbort("bad running of bwmake");
struct hash *sizeHash = readCsizeHash(argv[1]);
writeBw(argv[2], argv[3], sizeHash);
hashFree(&sizeHash);
return 0;
}
void bwtool_shift(struct hash *options, char *favorites, char *regions, unsigned decimals, enum wigOutType wot,
boolean condense, char *val_s, char *bigfile, char *tmp_dir, char *outputfile)
/* bwtool_shift - main for shifting program */
{
const double na = NANUM;
int shft = sqlSigned(val_s);
int abs_shft = abs(shft);
struct metaBig *mb = metaBigOpen_check(bigfile, tmp_dir, regions);
if (!mb)
errAbort("problem opening %s", bigfile);
char wigfile[512];
safef(wigfile, sizeof(wigfile), "%s.tmp.wig", outputfile);
FILE *out = mustOpen(wigfile, "w");
struct bed *section;
boolean up = TRUE;
if (shft > 0)
up = FALSE;
if (shft == 0)
errAbort("it doesn't make sense to shift by zero.");
for (section = mb->sections; section != NULL; section = section->next)
{
struct perBaseWig *pbw = perBaseWigLoadSingleContinue(mb, section->chrom, section->chromStart,
section->chromEnd, FALSE, na);
int i;
/* if the shift size is bigger than the section, NA the entire thing */
int size = pbw->len;
if (abs_shft >= size)
for (i = 0; i < size; i++)
pbw->data[i] = na;
else
{
if (!up)
{
for (i = size-1; i >= abs_shft; i--)
pbw->data[i] = pbw->data[i - abs_shft];
for (; i >= 0; i--)
pbw->data[i] = na;
}
else
{
for (i = 0; i < size - abs_shft; i++)
pbw->data[i] = pbw->data[i + abs_shft];
for (; i < size; i++)
pbw->data[i] = na;
}
}
perBaseWigOutputNASkip(pbw, out, wot, decimals, NULL, FALSE, condense);
perBaseWigFree(&pbw);
}
carefulClose(&out);
writeBw(wigfile, outputfile, mb->chromSizeHash);
remove(wigfile);
metaBigClose(&mb);
}
void bwtool_lift(struct hash *options, char *favorites, char *regions, unsigned decimals,
enum wigOutType wot, char *bigfile, char *chainfile, char *outputfile)
/* bwtool_lift - main for lifting program */
{
struct hash *sizeHash = NULL;
struct hash *chainHash = readLiftOverMapChainHash(chainfile);
struct hash *gpbw = NULL;
char *size_file = hashFindVal(options, "sizes");
char *bad_file = hashFindVal(options, "unlifted");
if (size_file)
sizeHash = readCsizeHash(size_file);
else
sizeHash = qSizeHash(chainfile);
gpbw = genomePbw(sizeHash);
struct metaBig *mb = metaBigOpen_check(bigfile, regions);
char wigfile[512];
safef(wigfile, sizeof(wigfile), "%s.tmp.wig", outputfile);
FILE *out = mustOpen(wigfile, "w");
struct hashEl *elList = hashElListHash(gpbw);
struct hashEl *el;
verbose(2,"starting first pass\n");
do_pass1(mb, chainHash, gpbw);
verbose(2, "starting second pass\n");
do_pass2(mb, chainHash, gpbw);
verbose(2,"starting final pass\n");
do_final_pass(mb, chainHash, gpbw, bad_file);
slSort(&elList, pbwHashElCmp);
for (el = elList; el != NULL; el = el->next)
{
struct perBaseWig *pbw = (struct perBaseWig *)el->val;
perBaseWigOutputNASkip(pbw, out, wot, decimals, NULL, FALSE, FALSE);
}
hashElFreeList(&elList);
carefulClose(&out);
hashFreeWithVals(&chainHash, freeChainHashMap);
hashFreeWithVals(&gpbw, perBaseWigFree);
writeBw(wigfile, outputfile, sizeHash);
hashFree(&sizeHash);
remove(wigfile);
metaBigClose(&mb);
}
void bwtool_fill(struct hash *options, char *favorites, char *regions, unsigned decimals, enum wigOutType wot,
boolean condense, char *val_s, char *bigfile, char *tmp_dir, char *outputfile)
/* bwtool_fill - main for filling program */
{
double val = sqlDouble(val_s);
struct metaBig *mb = metaBigOpen_check(bigfile, tmp_dir, regions);
char wigfile[512];
safef(wigfile, sizeof(wigfile), "%s.tmp.wig", outputfile);
FILE *out = mustOpen(wigfile, "w");
struct bed *section;
int i;
for (section = mb->sections; section != NULL; section = section->next)
{
struct perBaseWig *pbw = perBaseWigLoadSingleContinue(mb, section->chrom, section->chromStart,
section->chromEnd, FALSE, val);
perBaseWigOutput(pbw, out, wot, decimals, NULL, FALSE, condense);
perBaseWigFree(&pbw);
}
carefulClose(&out);
writeBw(wigfile, outputfile, mb->chromSizeHash);
remove(wigfile);
metaBigClose(&mb);
}
