void TextItem::mouseReleaseEvent(QGraphicsSceneMouseEvent *event)
{
QGraphicsItem::mouseReleaseEvent(event);
if (isSelected() && (flags() & QGraphicsItem::ItemIsMovable) && positionChanged) {
InsertData insertData = meta.value();
qreal topLeft[2] = { sceneBoundingRect().left(), sceneBoundingRect().top() };
qreal size[2] = { sceneBoundingRect().width(), sceneBoundingRect().height() };
PlacementData pld;
pld.placement = TopLeft;
pld.justification = Center;
pld.relativeTo = PageType;
pld.preposition = Inside;
calcOffsets(pld,insertData.offsets,topLeft,size);
QStringList list = toPlainText().split("\n");
insertData.text = list.join("\\n");
meta.setValue(insertData);
beginMacro(QString("MoveText"));
changeInsertOffset(&meta);
endMacro();
}
}
void LLVertexBuffer::updateNumVerts(S32 nverts)
{
LLMemType mt(LLMemType::MTYPE_VERTEX_DATA);
llassert(nverts >= 0);
if (nverts >= 65535)
{
llwarns << "Vertex buffer overflow!" << llendl;
nverts = 65535;
}
mRequestedNumVerts = nverts;
if (!mDynamicSize)
{
mNumVerts = nverts;
}
else if (mUsage == GL_STATIC_DRAW_ARB ||
nverts > mNumVerts ||
nverts < mNumVerts/2)
{
if (mUsage != GL_STATIC_DRAW_ARB && nverts + nverts/4 <= 65535)
{
nverts += nverts/4;
}
mNumVerts = nverts;
}
mSize = calcOffsets(mTypeMask, mOffsets, mNumVerts);
}
/* Calculate all offset in font set. Start by assuming the best possible case
where all variable-length offsets are 1-byte long and calculate sizes and
offsets. Then recalculate all sizes and offsets and iterate until there are
no further changes. */
static void fillOffsets(tcprivCtx h) {
int i;
/* Initialize header */
h->cffHdr.major = TC_MAJOR;
h->cffHdr.minor = TC_MINOR;
h->cffHdr.offSize = 1;
/* Compute initial font sizes */
h->size.FontNames = 0;
h->size.dicts = 0;
h->size.gsubrs = subrSizeGlobal(h->g);
for (i = 0; i < h->set.cnt; i++) {
fillInitialSizes(h, &h->set.array[i]);
}
h->size.nameINDEX = INDEX_SIZE(h->set.cnt, h->size.FontNames);
h->size.dictINDEX = INDEX_SIZE(h->set.cnt, h->size.dicts);
/* Iterate offset computation until final offset remains unchanged */
h->offset.copyright = 0;
while (calcOffsets(h)) {
calcSizes(h);
}
h->cffHdr.hdrSize = CFF_HEADER_SIZE;
/* Fill index headers */
h->nameHdr.count = (unsigned short)h->set.cnt;
h->nameHdr.offSize = INDEX_OFF_SIZE(h->size.FontNames);
h->dictHdr.count = (unsigned short)h->set.cnt;
h->dictHdr.offSize = INDEX_OFF_SIZE(h->size.dicts);
/* Add offsets to dictionaries */
for (i = 0; i < h->set.cnt; i++) {
Font *font = &h->set.array[i];
if (font->offset.encoding != 0) {
/* Save encoding offset */
dictSaveInt(&font->dict, font->offset.encoding);
DICTSAVEOP(font->dict, cff_Encoding);
}
if (!(font->flags & FONT_SYNTHETIC)) {
if (font->offset.charset != 0) {
/* Save charset offset */
dictSaveInt(&font->dict, font->offset.charset);
DICTSAVEOP(font->dict, cff_charset);
}
if (!(font->flags & FONT_CHAMELEON)) {
/* Save CharString offset */
dictSaveInt(&font->dict, font->offset.CharStrings);
DICTSAVEOP(font->dict, cff_CharStrings);
}
if (font->flags & FONT_CID) {
int j;
/* Save FDSelect offset */
dictSaveInt(&font->dict, font->offset.fdselect);
DICTSAVEOP(font->dict, cff_FDSelect);
/* Save FDArray offset */
dictSaveInt(&font->dict, font->offset.FDArray);
DICTSAVEOP(font->dict, cff_FDArray);
for (j = 0; j < font->fdCount; j++) {
FDInfo *fdInfo = &font->fdInfo[j];
if (fdInfo->seenChar) {
/* Save Private sizes/offsets */
dictSaveInt(&fdInfo->FD, fdInfo->size.Private);
dictSaveInt(&fdInfo->FD, fdInfo->offset.Private);
DICTSAVEOP(fdInfo->FD, cff_Private);
if (fdInfo->size.Subrs != 0) {
/* Save Subrs offset */
dictSaveInt(&fdInfo->Private, fdInfo->offset.Subrs);
DICTSAVEOP(fdInfo->Private, cff_Subrs);
}
}
}
} else {
/* Save Private size/offset */
dictSaveInt(&font->dict, font->size.Private);
dictSaveInt(&font->dict, font->offset.Private);
DICTSAVEOP(font->dict, cff_Private);
if (font->size.Subrs != 0) {
/* Save Subrs offset */
dictSaveInt(&font->Private, font->offset.Subrs);
DICTSAVEOP(font->Private, cff_Subrs);
}
}
}
}
}
int main(int argc, char **argv)
{
if (argc < 4)
errx(1,
"usage\t:%s <bam> <split out> <discord out> (optional #threads)",
argv[0]);
char *bam_file_name = argv[1];
char *split_file_name = argv[2];
char *disc_file_name = argv[3];
int threads = 2;
if (argc == 5) {
threads = atoi(argv[4]);
}
samFile *disc = sam_open(disc_file_name, "wb");
samFile *split = sam_open(split_file_name, "wb");
samFile *in = sam_open(bam_file_name, "rb");
if(in == NULL)
errx(1, "Unable to open BAM/SAM file.");
// TODO: handle cram.
if (threads > 1) {
bgzf_mt(in->fp.bgzf, threads, 256);
}
hts_idx_t *idx = sam_index_load(in, bam_file_name);
if(idx == NULL)
errx(1,"Unable to open BAM/SAM index.");
bam_hdr_t *hdr = sam_hdr_read(in);
int r = sam_hdr_write(disc, hdr);
r = sam_hdr_write(split, hdr);
bam1_t *aln = bam_init1();
int ret;
while(ret = sam_read1(in, hdr, aln) >= 0) {
if (((aln->core.flag) & 1294) == 0)
r = sam_write1(disc, hdr, aln);
uint8_t *sa = bam_aux_get(aln, "SA");
if (sa != 0) {
char *sa_tag = strdup(bam_aux2Z(sa));
if ( count_tags(sa_tag) == 1) {
char *chrm, strand, *cigar;
uint32_t pos;
split_sa_tag(sa_tag,
&chrm,
&pos,
&strand,
&cigar);
struct line sa, al;
calcOffsets(cigar,
pos,
strand,
&sa);
sa.chrm = chrm;
sa.strand = strand;
calcAlnOffsets(bam_get_cigar(aln),
aln->core.n_cigar,
aln->core.pos,
bam_is_rev(aln) ? '-' : '+',
&al);
al.chrm = hdr->target_name[aln->core.tid];
al.strand = bam_is_rev(aln) ? '-' : '+';
struct line *left = &al, *right = &sa;
if (left->SQO > right->SQO) {
left = &sa;
right = &al;
}
int overlap = MAX(1 + MIN(left->EQO, right->EQO) -
MAX(left->SQO, right->SQO), 0);
int alen1 = 1 + left->EQO - left->SQO;
int alen2 = 1 + right->EQO - right->SQO;
int mno = MIN(alen1-overlap, alen2-overlap);
if (mno < MIN_NON_OVERLAP)
continue;
if ( (strcmp(left->chrm, right->chrm) == 0) &&
(left->strand == right->strand) ) {
int leftDiag, rightDiag, insSize;
if (left->strand == '-') {
leftDiag = left->rapos - left->sclip;
rightDiag = (right->rapos + right->raLen) -
(right->sclip + right->qaLen);
insSize = rightDiag - leftDiag;
} else {
leftDiag = (left->rapos + left->raLen) -
(left->sclip + left->qaLen);
rightDiag = right->rapos - right->sclip;
insSize = leftDiag - rightDiag;
}
int desert = right->SQO - left->EQO - 1;
if ((abs(insSize) < MIN_INDEL_SIZE) ||
((desert > 0) && (
(desert - (int)MAX(0, insSize)) >
MAX_UNMAPPED_BASES)))
continue;
}
char *qname = bam_get_qname(aln);
if ((aln->core.flag & 64) == 64)
qname[0] = 'A';
else
qname[0] = 'B';
r = sam_write1(split, hdr, aln);
}
free(sa_tag);
}
}
bam_destroy1(aln);
hts_idx_destroy(idx);
bam_hdr_destroy(hdr);
sam_close(in);
sam_close(disc);
sam_close(split);
if(ret < -1) {
errx(1, "lumpy_filter: error reading bam: %s\n", bam_file_name);
}
}
