[med-svn] [Git][med-team/rapmap][master] 10 commits: New upstream version
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Nov 14 13:46:45 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / rapmap
Commits:
f3ddec25 by Michael R. Crusoe at 2019-11-14T13:38:26Z
New upstream version
- - - - -
9e3b41dd by Michael R. Crusoe at 2019-11-14T13:38:27Z
New upstream version 0.15.0+dfsg
- - - - -
5c3d4b6c by Michael R. Crusoe at 2019-11-14T13:38:30Z
Update upstream source from tag 'upstream/0.15.0+dfsg'
Update to upstream version '0.15.0+dfsg'
with Debian dir 97b5fc7d96904bf4878208199961633944718f29
- - - - -
4c01b9b0 by Michael R. Crusoe at 2019-11-14T13:38:30Z
debhelper-compat 12
- - - - -
b0dd3369 by Michael R. Crusoe at 2019-11-14T13:38:33Z
Standards-Version: 4.4.0
- - - - -
14b9d906 by Michael R. Crusoe at 2019-11-14T13:38:36Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
4fe6b38f by Michael R. Crusoe at 2019-11-14T13:38:38Z
Set upstream metadata fields: Repository.
- - - - -
c733c9f3 by Michael R. Crusoe at 2019-11-14T13:40:57Z
make python3 build-dep explicit
- - - - -
332c8143 by Michael R. Crusoe at 2019-11-14T13:44:17Z
-dev, -examples are Multi-Arch: foreign
- - - - -
551977fa by Michael R. Crusoe at 2019-11-14T13:45:34Z
release
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/rules
- debian/upstream/metadata
- include/IndexHeader.hpp
- src/RapMapSAIndexer.cpp
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+rapmap (0.15.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Trim trailing whitespace.
+ * Set upstream metadata fields: Repository.
+ * -dev, -examples are Multi-Arch: foreign
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 14 Nov 2019 14:45:15 +0100
+
rapmap (0.14.1+dfsg-2) unstable; urgency=medium
* only amd64 due to compiling variants for Intel SSE extensions
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper-compat (= 12),
cmake,
zlib1g-dev,
libdivsufsort-dev,
@@ -15,8 +15,9 @@ Build-Depends: debhelper (>= 11),
libspdlog-dev,
libtclap-dev,
pkg-config,
- python3-markdown
-Standards-Version: 4.3.0
+ python3-markdown,
+ python3
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/rapmap
Vcs-Git: https://salsa.debian.org/med-team/rapmap.git
Homepage: https://github.com/COMBINE-lab/RapMap
@@ -52,6 +53,7 @@ Description: rapid sensitive and accurate DNA read mapping via quasi-mapping
Package: rapmap-example-data
Architecture: all
+Multi-Arch: foreign
Depends: ${misc:Depends}
Recommends: rapmap
Description: example data for rapmap - rapid sensitive and accurate DNA read mapping
@@ -70,6 +72,7 @@ Description: example data for rapmap - rapid sensitive and accurate DNA read map
Package: rapmap-dev
Architecture: all
+Multi-Arch: foreign
Depends: ${misc:Depends}
Description: rapmap - rapid sensitive and accurate DNA read mapping (some headers)
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
=====================================
debian/rules
=====================================
@@ -24,5 +24,3 @@ override_dh_auto_build:
override_dh_clean:
dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam
-
-
=====================================
debian/upstream/metadata
=====================================
@@ -1,33 +1,33 @@
Reference:
- - Author: Avi Srivastava and Hirak Sarkar and Nitish Gupta and Rob Patro
- Title: >
- RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to
- transcriptomes
- Journal: Bioinformatics
- Year: 2016
- Volume: 32
- Number: 12
- Pages: i192-i200
- DOI: 10.1093/bioinformatics/btw277
- PMID: 27307617
- URL: http://bioinformatics.oxfordjournals.org/content/32/12/i192
- eprint: http://bioinformatics.oxfordjournals.org/content/32/12/i192.full.pdf
- - Author: Nicolas L Bray and Harold Pimentel and Páll Melsted and Lior Pachter
- Title: "Near-optimal probabilistic RNA-seq quantification"
- Journal: Nature biotechnology
- Year: 2016
- Volume: 34
- Number: 5
- Pages: 525-527
- DOI: 10.1038/nbt.3519
- PMID: 27043002
- URL: http://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html
+- Author: Avi Srivastava and Hirak Sarkar and Nitish Gupta and Rob Patro
+ Title: "RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to\
+ \ transcriptomes\n"
+ Journal: Bioinformatics
+ Year: 2016
+ Volume: 32
+ Number: 12
+ Pages: i192-i200
+ DOI: 10.1093/bioinformatics/btw277
+ PMID: 27307617
+ URL: http://bioinformatics.oxfordjournals.org/content/32/12/i192
+ eprint: http://bioinformatics.oxfordjournals.org/content/32/12/i192.full.pdf
+- Author: Nicolas L Bray and Harold Pimentel and Páll Melsted and Lior Pachter
+ Title: "Near-optimal probabilistic RNA-seq quantification"
+ Journal: Nature biotechnology
+ Year: 2016
+ Volume: 34
+ Number: 5
+ Pages: 525-527
+ DOI: 10.1038/nbt.3519
+ PMID: 27043002
+ URL: http://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html
Registry:
- - Name: OMICtools
- Entry: OMICS_10349
- - Name: bio.tools
- Entry: rapmap
- - Name: SciCrunch
- Entry: NA
- - Name: conda:bioconda
- Entry: rapmap
+- Name: OMICtools
+ Entry: OMICS_10349
+- Name: bio.tools
+ Entry: rapmap
+- Name: SciCrunch
+ Entry: NA
+- Name: conda:bioconda
+ Entry: rapmap
+Repository: https://github.com/COMBINE-lab/RapMap
=====================================
include/IndexHeader.hpp
=====================================
@@ -54,6 +54,8 @@ class IndexHeader {
ar( cereal::make_nvp("NameHash", nameHash256_) );
ar( cereal::make_nvp("SeqHash512", seqHash512_) );
ar( cereal::make_nvp("NameHash512", nameHash512_) );
+ ar( cereal::make_nvp("DecoySeqHash", decoySeqHash256_) );
+ ar( cereal::make_nvp("DecoyNameHash", decoyNameHash256_) );
}
template <typename Archive>
@@ -69,6 +71,8 @@ class IndexHeader {
ar( cereal::make_nvp("NameHash", nameHash256_) );
ar( cereal::make_nvp("SeqHash512", seqHash512_) );
ar( cereal::make_nvp("NameHash512", nameHash512_) );
+ ar( cereal::make_nvp("DecoySeqHash", decoySeqHash256_) );
+ ar( cereal::make_nvp("DecoyNameHash", decoyNameHash256_) );
} catch (const cereal::Exception& e) {
auto cerrLog = spdlog::get("stderrLog");
cerrLog->error("Encountered exception [{}] when loading index.", e.what());
@@ -91,10 +95,16 @@ class IndexHeader {
std::string seqHash256() const { return seqHash256_; }
std::string nameHash256() const { return nameHash256_; }
+ void setDecoySeqHash256(const std::string& seqHash) { decoySeqHash256_ = seqHash; }
+ void setDecoyNameHash256(const std::string& nameHash) { decoyNameHash256_ = nameHash; }
+ std::string decoySeqHash256() const { return decoySeqHash256_; }
+ std::string decoyNameHash256() const { return decoyNameHash256_; }
+
void setSeqHash512(const std::string& seqHash) { seqHash512_ = seqHash; }
void setNameHash512(const std::string& nameHash) { nameHash512_ = nameHash; }
std::string seqHash512() const { return seqHash512_; }
std::string nameHash512() const { return nameHash512_; }
+
private:
// The type of index we have
IndexType type_;
@@ -117,6 +127,10 @@ class IndexHeader {
std::string seqHash512_;
// Hash of sequence names in txome
std::string nameHash512_;
+ // Hash of the names of decoys
+ std::string decoyNameHash256_;
+ // Hash of the sequences of decoys
+ std::string decoySeqHash256_;
};
=====================================
src/RapMapSAIndexer.cpp
=====================================
@@ -465,8 +465,11 @@ void indexTranscriptsSA(ParserT* parser,
digestpp::sha256 nameHasher256;
digestpp::sha512 seqHasher512;
digestpp::sha512 nameHasher512;
- //picosha2::hash256_one_by_one seqHasher; seqHasher.init();
- //picosha2::hash256_one_by_one nameHasher; nameHasher.init();
+
+ digestpp::sha256 decoySeqHasher256;
+ digestpp::sha256 decoyNameHasher256;
+
+
bool firstRecord{true};
bool hasGencodeSep = (sepStr.find('|') != std::string::npos);
@@ -536,9 +539,6 @@ void indexTranscriptsSA(ParserT* parser,
[](const char a) -> bool { return !(isprint(a)); }),
readStr.end());
- seqHasher256.absorb(readStr.begin(), readStr.end());
- seqHasher512.absorb(readStr.begin(), readStr.end());
-
uint32_t readLen = readStr.size();
uint32_t completeLen = readLen;
@@ -573,6 +573,14 @@ void indexTranscriptsSA(ParserT* parser,
//throw std::logic_error("Input fasta file contained out-of-order decoy targets.");
}
+ // If this was a decoy, add it to the decoy hash
+ if (isDecoy) {
+ decoySeqHasher256.absorb(readStr.begin(), readStr.end());
+ } else { // otherwise the ref hash
+ seqHasher256.absorb(readStr.begin(), readStr.end());
+ seqHasher512.absorb(readStr.begin(), readStr.end());
+ }
+
// First, replace non ATCG nucleotides
for (size_t b = 0; b < readLen; ++b) {
readStr[b] = ::toupper(readStr[b]);
@@ -656,8 +664,12 @@ void indexTranscriptsSA(ParserT* parser,
// If there was no collision, then add the transcript
transcriptNames.emplace_back(processedName);
- nameHasher256.absorb(processedName.begin(), processedName.end());
- nameHasher512.absorb(processedName.begin(), processedName.end());
+ if (isDecoy) {
+ decoyNameHasher256.absorb(processedName.begin(), processedName.end());
+ } else {
+ nameHasher256.absorb(processedName.begin(), processedName.end());
+ nameHasher512.absorb(processedName.begin(), processedName.end());
+ }
// The position at which this transcript starts
transcriptStarts.push_back(currIndex);
@@ -869,10 +881,15 @@ void indexTranscriptsSA(ParserT* parser,
std::string nameHash256 = nameHasher256.hexdigest();
std::string seqHash512 = seqHasher512.hexdigest();
std::string nameHash512 = nameHasher512.hexdigest();
+ std::string decoySeqHash256 = decoySeqHasher256.hexdigest();
+ std::string decoyNameHash256 = decoyNameHasher256.hexdigest();
+
header.setSeqHash256(seqHash256);
header.setNameHash256(nameHash256);
header.setSeqHash512(seqHash512);
header.setNameHash512(nameHash512);
+ header.setDecoySeqHash256(decoySeqHash256);
+ header.setDecoyNameHash256(decoyNameHash256);
//std::string seqHash;
//std::string nameHash;
//picosha2::get_hash_hex_string(seqHasher, seqHash);
View it on GitLab: https://salsa.debian.org/med-team/rapmap/compare/516e9dc76bad061954791ad90f8a275c448ca1fa...551977faf093118756a3c251d5aa8f688bcd1515
--
View it on GitLab: https://salsa.debian.org/med-team/rapmap/compare/516e9dc76bad061954791ad90f8a275c448ca1fa...551977faf093118756a3c251d5aa8f688bcd1515
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