[med-svn] [Git][med-team/libbigwig][master] 7 commits: New upstream version 0.4.8+dfsg
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Fri Aug 22 15:25:52 BST 2025
Steffen Möller pushed to branch master at Debian Med / libbigwig
Commits:
ca73cc86 by Steffen Moeller at 2025-08-22T16:00:17+02:00
New upstream version 0.4.8+dfsg
- - - - -
c5c3b58f by Steffen Moeller at 2025-08-22T16:00:17+02:00
New upstream version
- - - - -
ee6c2d40 by Steffen Moeller at 2025-08-22T16:00:17+02:00
Update upstream source from tag 'upstream/0.4.8+dfsg'
Update to upstream version '0.4.8+dfsg'
with Debian dir d1ed6c75d65fc00c109cef062dcac11ba03d1452
- - - - -
02042eba by Steffen Moeller at 2025-08-22T16:00:18+02:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
7ce37dad by Steffen Moeller at 2025-08-22T15:00:24+01:00
Remove unnecessary Team Upload line in changelog.
Changes-By: lintian-brush
- - - - -
22b8f476 by Steffen Moeller at 2025-08-22T15:00:27+01:00
Set upstream metadata fields: Registry.
Changes-By: lintian-brush
- - - - -
f03a9854 by Steffen Moeller at 2025-08-22T16:23:53+02:00
Preparing for upload.
- - - - -
11 changed files:
- bigWig.h
- bwStats.c
- bwValues.c
- bwWrite.c
- + debian/.gitignore
- debian/changelog
- debian/control
- − debian/libbigwig0t64.lintian-overrides
- − debian/libbigwig0t64.symbols
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
bigWig.h
=====================================
@@ -56,7 +56,7 @@ extern "C" {
/*!
* The library version number
*/
-#define LIBBIGWIG_VERSION 0.4.7
+#define LIBBIGWIG_VERSION 0.4.8
/*!
* If 1, then this library was compiled with remote file support.
=====================================
bwStats.c
=====================================
@@ -70,7 +70,7 @@ static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint
if(sz) {
compressed = 1;
- buf = malloc(sz);
+ buf = malloc(sz);
}
sz = 0; //This is now the size of the compressed buffer
@@ -96,7 +96,7 @@ static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint
}
p = buf;
- while(((uLongf) ((void*)p-buf)) < sz) {
+ while(((uLongf) ((char*)p - (char*)buf)) < sz) {
vtid = p[0];
vstart = p[1];
vend = p[2];
=====================================
bwValues.c
=====================================
@@ -135,8 +135,7 @@ static bwOverlapBlock_t *overlapsLeaf(bwRTreeNode_t *node, uint32_t tid, uint32_
if(!o) return NULL;
for(i=0; i<node->nChildren; i++) {
- if(tid < node->chrIdxStart[i]) break;
- if(tid > node->chrIdxEnd[i]) continue;
+ if(tid < node->chrIdxStart[i] || tid > node->chrIdxEnd[i]) continue;
/*
The individual blocks can theoretically span multiple contigs.
@@ -162,7 +161,6 @@ static bwOverlapBlock_t *overlapsLeaf(bwRTreeNode_t *node, uint32_t tid, uint32_
if(!o->size) goto error;
for(i=0; i<node->nChildren; i++) {
- if(tid < node->chrIdxStart[i]) break;
if(tid < node->chrIdxStart[i] || tid > node->chrIdxEnd[i]) continue;
if(node->chrIdxStart[i] != node->chrIdxEnd[i]) {
if(tid == node->chrIdxStart[i]) {
@@ -524,15 +522,15 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
tmp = o->size[i]; //TODO: Is this correct? Do non-gzipped bigBeds exist?
}
- bufEnd = buf + tmp;
+ bufEnd = (char*)buf + tmp;
while(buf < bufEnd) {
entryTid = ((uint32_t*)buf)[0];
start = ((uint32_t*)buf)[1];
end = ((uint32_t*)buf)[2];
- buf += 12;
+ buf = (char*)buf + 12;
str = (char*)buf;
slen = strlen(str) + 1;
- buf += slen;
+ buf = (char*)buf + slen;
if(entryTid < tid) continue;
if(entryTid > tid) break;
@@ -543,7 +541,7 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
if(!pushBBIntervals(output, start, end, str, withString)) goto error;
}
- buf = bufEnd - tmp; //reset the buffer pointer
+ buf = (char*)bufEnd - tmp; //reset the buffer pointer
}
if(compressed && buf) free(buf);
@@ -552,7 +550,7 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
error:
fprintf(stderr, "[bbGetOverlappingEntriesCore] Got an error\n");
- buf = bufEnd - tmp;
+ buf = (char*)bufEnd - tmp;
if(output) bbDestroyOverlappingEntries(output);
if(compressed && buf) free(buf);
if(compBuf) free(compBuf);
=====================================
bwWrite.c
=====================================
@@ -317,12 +317,12 @@ static int flushBuffer(bigWigFile_t *fp) {
if(!wb->ltype) return 0;
//Fill in the header
- if(!memcpy(wb->p, &(wb->tid), sizeof(uint32_t))) return 1;
- if(!memcpy(wb->p+4, &(wb->start), sizeof(uint32_t))) return 2;
- if(!memcpy(wb->p+8, &(wb->end), sizeof(uint32_t))) return 3;
- if(!memcpy(wb->p+12, &(wb->step), sizeof(uint32_t))) return 4;
- if(!memcpy(wb->p+16, &(wb->span), sizeof(uint32_t))) return 5;
- if(!memcpy(wb->p+20, &(wb->ltype), sizeof(uint8_t))) return 6;
+ if(!memcpy((char*)wb->p, &(wb->tid), sizeof(uint32_t))) return 1;
+ if(!memcpy((char*)wb->p+4, &(wb->start), sizeof(uint32_t))) return 2;
+ if(!memcpy((char*)wb->p+8, &(wb->end), sizeof(uint32_t))) return 3;
+ if(!memcpy((char*)wb->p+12, &(wb->step), sizeof(uint32_t))) return 4;
+ if(!memcpy((char*)wb->p+16, &(wb->span), sizeof(uint32_t))) return 5;
+ if(!memcpy((char*)wb->p+20, &(wb->ltype), sizeof(uint8_t))) return 6;
//1 byte padding
//Determine the number of items
switch(wb->ltype) {
@@ -338,7 +338,7 @@ static int flushBuffer(bigWigFile_t *fp) {
default:
return 7;
}
- if(!memcpy(wb->p+22, &nItems, sizeof(uint16_t))) return 8;
+ if(!memcpy((char*)wb->p+22, &nItems, sizeof(uint16_t))) return 8;
if(sz) {
//compress
@@ -399,9 +399,9 @@ int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *s
wb->span = 0;
wb->step = 0;
}
- if(!memcpy(wb->p+wb->l, start, sizeof(uint32_t))) return 7;
- if(!memcpy(wb->p+wb->l+4, end, sizeof(uint32_t))) return 8;
- if(!memcpy(wb->p+wb->l+8, values, sizeof(float))) return 9;
+ if(!memcpy((char*)wb->p+wb->l, start, sizeof(uint32_t))) return 7;
+ if(!memcpy((char*)wb->p+wb->l+4, end, sizeof(uint32_t))) return 8;
+ if(!memcpy((char*)wb->p+wb->l+8, values, sizeof(float))) return 9;
updateStats(fp, end[0]-start[0], values[0]);
wb->l += 12;
@@ -420,9 +420,9 @@ int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *s
flushBuffer(fp);
wb->start = start[i];
}
- if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 11;
- if(!memcpy(wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 12;
- if(!memcpy(wb->p+wb->l+8, &(values[i]), sizeof(float))) return 13;
+ if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 11;
+ if(!memcpy((char*)wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 12;
+ if(!memcpy((char*)wb->p+wb->l+8, &(values[i]), sizeof(float))) return 13;
updateStats(fp, end[i]-start[i], values[i]);
wb->l += 12;
}
@@ -447,9 +447,9 @@ int bwAppendIntervals(bigWigFile_t *fp, const uint32_t *start, const uint32_t *e
flushBuffer(fp);
wb->start = start[i];
}
- if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
- if(!memcpy(wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 5;
- if(!memcpy(wb->p+wb->l+8, &(values[i]), sizeof(float))) return 6;
+ if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
+ if(!memcpy((char*)wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 5;
+ if(!memcpy((char*)wb->p+wb->l+8, &(values[i]), sizeof(float))) return 6;
updateStats(fp, end[i]-start[i], values[i]);
wb->l += 12;
}
@@ -482,8 +482,8 @@ int bwAddIntervalSpans(bigWigFile_t *fp, const char *chrom, const uint32_t *star
flushBuffer(fp);
wb->start = start[i];
}
- if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 5;
- if(!memcpy(wb->p+wb->l+4, &(values[i]), sizeof(float))) return 6;
+ if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 5;
+ if(!memcpy((char*)wb->p+wb->l+4, &(values[i]), sizeof(float))) return 6;
updateStats(fp, span, values[i]);
wb->l += 8;
}
@@ -506,8 +506,8 @@ int bwAppendIntervalSpans(bigWigFile_t *fp, const uint32_t *start, const float *
flushBuffer(fp);
wb->start = start[i];
}
- if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
- if(!memcpy(wb->p+wb->l+4, &(values[i]), sizeof(float))) return 5;
+ if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
+ if(!memcpy((char*)wb->p+wb->l+4, &(values[i]), sizeof(float))) return 5;
updateStats(fp, wb->span, values[i]);
wb->l += 8;
}
@@ -540,7 +540,7 @@ int bwAddIntervalSpanSteps(bigWigFile_t *fp, const char *chrom, uint32_t start,
flushBuffer(fp);
wb->start = wb->end;
}
- if(!memcpy(wb->p+wb->l, &(values[i]), sizeof(float))) return 5;
+ if(!memcpy((char*)wb->p+wb->l, &(values[i]), sizeof(float))) return 5;
updateStats(fp, wb->span, values[i]);
wb->l += 4;
}
@@ -563,7 +563,7 @@ int bwAppendIntervalSpanSteps(bigWigFile_t *fp, const float *values, uint32_t n)
flushBuffer(fp);
wb->start = wb->end;
}
- if(!memcpy(wb->p+wb->l, &(values[i]), sizeof(float))) return 4;
+ if(!memcpy((char*)wb->p+wb->l, &(values[i]), sizeof(float))) return 4;
updateStats(fp, wb->span, values[i]);
wb->l += 4;
}
@@ -754,7 +754,7 @@ int writeIndex(bigWigFile_t *fp) {
}
if(!root) return 4;
fp->idx->root = root;
-
+
ll = fp->writeBuffer->firstIndexNode;
while(ll) {
p = ll->next;
@@ -994,8 +994,8 @@ int addIntervalValue(bigWigFile_t *fp, uint64_t *nEntries, double *sum, double *
newBuffer->p = calloc(itemsPerSlot, 32);
if(!newBuffer->p) goto error;
newBuffer->m = itemsPerSlot*32;
- memcpy(newBuffer->p, buffer->p+buffer->l-32, 4);
- memcpy(newBuffer->p+4, buffer->p+buffer->l-28, 4);
+ memcpy(newBuffer->p, (unsigned char*)buffer->p+buffer->l-32, 4);
+ memcpy((unsigned char*)newBuffer->p+4, (unsigned char*)buffer->p + buffer->l-28, 4);
((uint32_t*) newBuffer->p)[2] = ((uint32_t*) newBuffer->p)[1] + zoom;
*sum = *sumsq = 0.0;
rv = updateInterval(fp, newBuffer, sum, sumsq, zoom, tid, start, end, value);
@@ -1122,7 +1122,7 @@ int writeZoomLevels(bigWigFile_t *fp) {
while(ll) {
p = ll->next;
free(ll);
- ll=p;
+ ll=p;
}
=====================================
debian/.gitignore
=====================================
@@ -0,0 +1,2 @@
+/.debhelper
+/*.log
=====================================
debian/changelog
=====================================
@@ -1,9 +1,17 @@
-libbigwig (0.4.7+dfsg-4) UNRELEASED; urgency=medium
+libbigwig (0.4.8+dfsg-1) unstable; urgency=medium
- * Team upload.
+ [ Michael R. Crusoe ]
* d/control: move the -docs package to the docs section.
- -- Michael R. Crusoe <crusoe at debian.org> Wed, 05 Feb 2025 14:32:03 +0100
+ [ Steffen Möller ]
+ * New upstream version
+ * Standards-Version: 4.7.2 (routine-update)
+ Set upstream metadata fields: Registry.
+ * Fixed borked d/u/metadata
+ * Binary package name libbigwig0t64 to libbigwig0
+ * added d/.gitignore
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 22 Aug 2025 16:01:25 +0200
libbigwig (0.4.7+dfsg-3.1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -8,16 +8,15 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
libcurl4-gnutls-dev|libcurl-dev,
zlib1g-dev
Build-Depends-Indep: doxygen
-Standards-Version: 4.6.1
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/libbigwig
Vcs-Git: https://salsa.debian.org/med-team/libbigwig.git
Homepage: https://github.com/dpryan79/libBigWig/
Rules-Requires-Root: no
-Package: libbigwig0t64
+Package: libbigwig0
Provides: ${t64:Provides}
Replaces: libbigwig0
-Conflicts: libbigwig0 (<< ${source:Version})
Architecture: any
Section: libs
Multi-Arch: same
@@ -34,7 +33,7 @@ Package: libbigwig-dev
Architecture: any
Multi-Arch: same
Section: libdevel
-Depends: libbigwig0t64 (= ${binary:Version}),
+Depends: libbigwig0 (= ${binary:Version}),
${misc:Depends}
Description: C library for handling bigWig files - header files
This package provides the files needed to develop with the libBigWig
=====================================
debian/libbigwig0t64.lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-libbigwig0t64: package-name-doesnt-match-sonames libbigwig0
=====================================
debian/libbigwig0t64.symbols deleted
=====================================
@@ -1,66 +0,0 @@
-libBigWig.so.0 libbigwig0t64 #MINVER#
- GLOBAL_DEFAULTBUFFERSIZE at Base 0.4.6
- addIntervalValue at Base 0.4.6
- bbDestroyOverlappingEntries at Base 0.4.6
- bbGetOverlappingEntries at Base 0.4.6
- bbGetOverlappingEntriesCore at Base 0.4.6
- bbGetSQL at Base 0.4.6
- bbIsBigBed at Base 0.4.6
- bbOpen at Base 0.4.6
- bbOverlappingEntriesIterator at Base 0.4.6
- bwAddIntervalSpanSteps at Base 0.4.6
- bwAddIntervalSpans at Base 0.4.6
- bwAddIntervals at Base 0.4.6
- bwAppendIntervalSpanSteps at Base 0.4.6
- bwAppendIntervalSpans at Base 0.4.6
- bwAppendIntervals at Base 0.4.6
- bwCleanup at Base 0.4.6
- bwClose at Base 0.4.6
- bwCreateChromList at Base 0.4.6
- bwCreateHdr at Base 0.4.6
- bwDestroyIndex at Base 0.4.6
- bwDestroyIndexNode at Base 0.4.6
- bwDestroyOverlappingIntervals at Base 0.4.6
- bwFillBuffer at Base 0.4.6
- bwFillDataHdr at Base 0.4.6
- bwFinalize at Base 0.4.6
- bwGetOverlappingIntervals at Base 0.4.6
- bwGetOverlappingIntervalsCore at Base 0.4.6
- bwGetTid at Base 0.4.6
- bwGetValues at Base 0.4.6
- bwInit at Base 0.4.6
- bwIsBigWig at Base 0.4.6
- bwIteratorDestroy at Base 0.4.6
- bwIteratorNext at Base 0.4.6
- bwOpen at Base 0.4.6
- bwOverlappingIntervalsIterator at Base 0.4.6
- bwRead at Base 0.4.6
- bwReadIndex at Base 0.4.6
- bwSetPos at Base 0.4.6
- bwStats at Base 0.4.6
- bwStatsFromFull at Base 0.4.6
- bwStrdup at Base 0.4.7
- bwTell at Base 0.4.6
- bwWriteHdr at Base 0.4.6
- constructZoomLevels at Base 0.4.6
- destroyBWOverlapBlock at Base 0.4.6
- destroyVals_t at Base 0.4.6
- getContentLength at Base 0.4.6
- getScalar at Base 0.4.6
- makeZoomLevels at Base 0.4.6
- nextPos at Base 0.4.6
- overlapsInterval at Base 0.4.6
- updateInterval at Base 0.4.6
- urlClose at Base 0.4.6
- urlFetchData at Base 0.4.6
- urlOpen at Base 0.4.6
- urlRead at Base 0.4.6
- urlSeek at Base 0.4.6
- url_fread at Base 0.4.6
- walkRTreeNodes at Base 0.4.6
- writeIndex at Base 0.4.6
- writeIndexOffsets at Base 0.4.6
- writeIndexTree at Base 0.4.6
- writeIndexTreeNode at Base 0.4.6
- writeSummary at Base 0.4.6
- writeZoomLevels at Base 0.4.6
=====================================
debian/rules
=====================================
@@ -17,12 +17,11 @@ export DEB_CFLAGS_MAINT_APPEND = -D_FORTIFY_SOURCE=2
dh $@
override_dh_auto_build-indep:
- $(MAKE) doc
+ mkdir -p docs && $(MAKE) doc
override_dh_auto_install:
dh_auto_install
d-shlibmove --commit \
- --t64 \
--multiarch \
--devunversioned \
--exclude-la \
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+---
Bug-Database: https://github.com/dpryan79/libBigWig/issues
Bug-Submit: https://github.com/dpryan79/libBigWig/issues/new
Repository: https://github.com/dpryan79/libBigWig.git
@@ -7,4 +8,4 @@ Registry:
Entry: libbigwig
- Name: bio.tools
Entry: NA
- Checked: 2021-09-07
+ Checked: 2025-08-22
View it on GitLab: https://salsa.debian.org/med-team/libbigwig/-/compare/6d867d448539d4b47c9b6cb5bc7cbcc8bc5d18a8...f03a9854807836682b077760ada7ae53d1f82aab
--
View it on GitLab: https://salsa.debian.org/med-team/libbigwig/-/compare/6d867d448539d4b47c9b6cb5bc7cbcc8bc5d18a8...f03a9854807836682b077760ada7ae53d1f82aab
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20250822/bbdc4f54/attachment-0001.htm>
More information about the debian-med-commit
mailing list