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6
Avoid using non-public HTSlib headers and functions
· 820f035f
Andreas Tille
authored
Dec 18, 2019
820f035f
routine-update: Standards-Version: 4.4.1
· 44476aa7
Andreas Tille
authored
Dec 18, 2019
44476aa7
Set upstream metadata fields: Bug-Database.
· 722c79a3
Andreas Tille
authored
Dec 18, 2019
722c79a3
Refresh symbols
· 442e90ce
Andreas Tille
authored
Dec 18, 2019
442e90ce
do not (Build-)Depend libhts-private-dev
· ee6f2daf
Andreas Tille
authored
Dec 18, 2019
ee6f2daf
Upload to unstable
· b97d3004
Andreas Tille
authored
Dec 18, 2019
b97d3004
Show whitespace changes
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debian/changelog
View file @
b97d3004
libseqlib (1.1.2+dfsg-5) unstable; urgency=medium
* Avoid using non-public HTSlib headers and functions
and do not (Build-)Depend libhts-private-dev
Closes: #946924
* Standards-Version: 4.4.1
* Set upstream metadata fields: Bug-Database.
* Refresh symbols
-- Andreas Tille <tille@debian.org> Wed, 18 Dec 2019 14:17:13 +0100
libseqlib (1.1.2+dfsg-4) unstable; urgency=medium
* Adapt symbols to new version of gcc
...
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debian/control
View file @
b97d3004
...
...
@@ -6,14 +6,14 @@ Priority: optional
Build-Depends: debhelper-compat (= 12),
d-shlibs,
pkg-config,
libhts-
private-
dev,
libhts-dev,
libcurl4-openssl-dev | libcurl4-dev,
zlib1g-dev,
libfml-dev (>= 0.1-3),
libbwa-dev (>= 0.7.15-3),
libjsoncpp-dev,
libssw-dev
Standards-Version: 4.4.
0
Standards-Version: 4.4.
1
Vcs-Browser: https://salsa.debian.org/med-team/libseqlib
Vcs-Git: https://salsa.debian.org/med-team/libseqlib.git
Homepage: https://github.com/walaj/SeqLib
...
...
@@ -43,7 +43,6 @@ Depends: libseqlib1 (= ${binary:Version}),
${shlibs:Depends},
${misc:Depends},
libhts-dev (>= 1.3.2-3),
libhts-private-dev,
libjsoncpp-dev,
libbwa-dev,
libfml-dev,
...
...
debian/libseqlib1.symbols
View file @
b97d3004
...
...
@@ -126,10 +126,10 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZN6SeqLib8tostringIjEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 1.1.1+dfsg
_ZN6SeqLib9AddCommasIiEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 1.1.1+dfsg
_ZN6SeqLib9BamHeader21ConstructName2IDTableEv@Base 1.1.1+dfsg
_ZN6SeqLib9BamHeaderC1EPK9
b
am_hdr_t@Base 1.1.
1
+dfsg
_ZN6SeqLib9BamHeaderC1EPK9
s
am_hdr_t@Base 1.1.
2
+dfsg
_ZN6SeqLib9BamHeaderC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 1.1.1+dfsg
_ZN6SeqLib9BamHeaderC1ERKSt6vectorINS_14HeaderSequenceESaIS2_EE@Base 1.1.1+dfsg
_ZN6SeqLib9BamHeaderC2EPK9
b
am_hdr_t@Base 1.1.
1
+dfsg
_ZN6SeqLib9BamHeaderC2EPK9
s
am_hdr_t@Base 1.1.
2
+dfsg
_ZN6SeqLib9BamHeaderC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 1.1.1+dfsg
_ZN6SeqLib9BamHeaderC2ERKSt6vectorINS_14HeaderSequenceESaIS2_EE@Base 1.1.1+dfsg
_ZN6SeqLib9BamHeaderD1Ev@Base 1.1.1+dfsg
...
...
@@ -306,18 +306,18 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZNSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED0Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED1Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED2Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE14_M_get_deleterERKSt9type_info@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED0Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED1Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED2Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE14_M_get_deleterERKSt9type_info@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED0Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED1Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED2Ev@Base 1.1.1+dfsg
_ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base 1.1.2+dfsg
_ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv@Base 1.1.2+dfsg
_ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE14_M_get_deleterERKSt9type_info@Base 1.1.2+dfsg
_ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED0Ev@Base 1.1.2+dfsg
_ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED1Ev@Base 1.1.2+dfsg
_ZNSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EED2Ev@Base 1.1.2+dfsg
_ZNSt4pairIKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED1Ev@Base 1.1.1+dfsg
_ZNSt4pairIKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED2Ev@Base 1.1.1+dfsg
_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED1Ev@Base 1.1.1+dfsg
...
...
@@ -412,8 +412,8 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZTISt19_Sp_counted_deleterIP11__hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTISt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTISt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTISt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTISt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTISt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.2+dfsg
_ZTS10idx_delete@Base 1.1.1+dfsg
_ZTS14bam_hdr_delete@Base 1.1.1+dfsg
_ZTS14htsFile_delete@Base 1.1.1+dfsg
...
...
@@ -428,8 +428,8 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZTSSt19_Sp_counted_deleterIP11__hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTSSt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTSSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTSSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTSSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTSSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.2+dfsg
_ZTVSt15_Sp_counted_ptrIPN12aho_corasick10basic_trieIcEELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt15_Sp_counted_ptrIPSt13unordered_mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4hashIS6_ESt8equal_toIS6_ESaISt4pairIKS6_iEEELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIimEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
...
...
@@ -437,5 +437,5 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZTVSt19_Sp_counted_deleterIP11__hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt19_Sp_counted_deleterIP7htsFile14htsFile_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt19_Sp_counted_deleterIP9bam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.1+dfsg
_ZTVSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE@Base 1.1.2+dfsg
debian/patches/fix_private_htslib_usage.patch
0 → 100644
View file @
b97d3004
Author: John Marshall <John.W.Marshall@glasgow.ac.uk>
Date: Tue Dec 17 19:10:47 2019 +0000
Origin: https://github.com/walaj/SeqLib/commit/3fc64616a64adfcaf5271ae24f35e443ce822faf.patch
Bug-Debian: https://bugs.debian.org/946924
Description: Avoid using non-public HTSlib headers and functions
Only headers in htslib/*.h are part of HTSlib's public API; cram/*.h
in particular are not. Fortunately SeqLib only uses one function from
cram/cram_io.h, and that is easily replaced with a public equivalent.
Instead use `hts_set_fai_filename()`, which strdups the string given to
it itself; `cram_set_option(fp->fp.cram, CRAM_OPT_REFERENCE, ...)` would
also be an option, but it's better to avoid `fp->fp.cram` as poking into
an htsFile's insides is also not supported by HTSlib.
--- a/SeqLib/BamWalker.h
+++ b/SeqLib/BamWalker.h
@@ -11,11 +11,6 @@
#define INT32_MAX 0x7fffffffL
#endif
-extern "C" {
-#include "htslib/cram/cram.h"
-#include "htslib/cram/cram_io.h"
-}
-
struct idx_delete {
void operator()(hts_idx_t* x) { if (x) hts_idx_destroy(x); }
};
--- a/src/BamReader.cpp
+++ b/src/BamReader.cpp
@@ -186,9 +186,7 @@
BamReader::BamReader() {}
// open cram reference
if (!m_cram_reference.empty()) {
- char * m_cram_reference_cstr = strdup(m_cram_reference.c_str());
- int ret = cram_load_reference(fp->fp.cram, m_cram_reference_cstr);
- free(m_cram_reference_cstr);
+ int ret = hts_set_fai_filename(fp.get(), m_cram_reference.c_str());
if (ret < 0)
throw std::invalid_argument("Could not read reference genome " + m_cram_reference + " for CRAM opt");
}
debian/patches/series
View file @
b97d3004
...
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@@ -7,4 +7,5 @@ dynamic_lib.patch
use_debian_packaged_jsoncpp.patch
use_debian_packaged_ssw.patch
pkg-config.patch
use_private_htslib_headers.patch
# use_private_htslib_headers.patch
fix_private_htslib_usage.patch
debian/upstream/metadata
View file @
b97d3004
...
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@@ -7,9 +7,7 @@ Reference:
Year: 2016
DOI: 10.1093/bioinformatics/btw741
PMID: 28011768
URL: "https://academic.oup.com/bioinformatics/article-abstract/doi/\
10.1093/bioinformatics/btw741/2571356/\
SeqLib-a-C-API-for-rapid-BAM-manipulation-sequence"
URL: https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btw741/2571356/SeqLib-a-C-API-for-rapid-BAM-manipulation-sequence
Registry:
- Name: OMICtools
Entry: OMICS_14682
...
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@@ -17,3 +15,4 @@ Registry:
Entry: NA
- Name: bio.tools
Entry: NA
Bug-Database: https://github.com/walaj/SeqLib/issues
Andreas Tille authored
Andreas Tille authored
Andreas Tille authored
Andreas Tille authored
Andreas Tille authored
Andreas Tille authored