[med-svn] [Git][med-team/covtobed][master] 5 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Sun Oct 25 20:54:49 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / covtobed
Commits:
7d8b9a86 by Nilesh Patra at 2020-10-26T02:14:09+05:30
routine-update: New upstream version
- - - - -
e378a0cd by Nilesh Patra at 2020-10-26T02:14:17+05:30
New upstream version 1.2.0+dfsg
- - - - -
7a9b2740 by Nilesh Patra at 2020-10-26T02:14:49+05:30
Update upstream source from tag 'upstream/1.2.0+dfsg'
Update to upstream version '1.2.0+dfsg'
with Debian dir 3c718954f69fbb1181118fc9fcf91d48a980542a
- - - - -
7ea23558 by Nilesh Patra at 2020-10-26T02:16:28+05:30
Add myself to uploaders
- - - - -
eb142ae7 by Nilesh Patra at 2020-10-26T02:20:43+05:30
Update changelog
- - - - -
4 changed files:
- README.md
- base.cpp
- debian/changelog
- debian/control
Changes:
=====================================
README.md
=====================================
@@ -1,12 +1,14 @@
# covtobed
-[](https://github.com/telatin/covtobed/blob/master/LICENSE)
-[](http://bioconda.github.io/recipes/covtobed/README.html)
+
+[](http://bioconda.github.io/recipes/covtobed/README.html)
[](https://anaconda.org/bioconda/covtobed)
[](https://travis-ci.org/telatin/covtobed)
-[](https://hub.docker.com/r/andreatelatin/covtobed)
+[](https://hub.docker.com/r/andreatelatin/covtobed)
[](https://www.codacy.com/manual/telatin/covtobed?utm_source=github.com&utm_medium=referral&utm_content=telatin/covtobed&utm_campaign=Badge_Grade)
+
[](https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b)
+[](https://github.com/telatin/covtobed/blob/master/LICENSE)
### a tool to generate BED coverage tracks from BAM files
@@ -15,6 +17,10 @@ Reads one (or more) [alignment](https://en.wikipedia.org/wiki/Sequence_alignment
:book: **[Read more in the wiki](https://github.com/telatin/covtobed/wiki)** - this is the **main** documentation source
+Features:
+* Can read (sorted) BAMs from stream (like `bwa mem .. | samtools view -b | samtools sort - | covtobed`)
+* Can print _strand specific_ coverage to check for strand imbalance
+* Can print the _physical coverage_ (with paired-end or mate-paired libraries)
[](https://github.com/telatin/covtobed/wiki)
@@ -45,6 +51,8 @@ Options:
-l MINLEN, --min-len=MINLEN
print BED feature only if its length is bigger (or equal
to) than MINLELN (default: 1)
+ -z MINCTG, --min-ctg-len=MINCTG
+ skip reference sequences having size less or equal to MINCTG
-d, --discard-invalid-alignments
skip duplicates, failed QC, and non primary alignment,
minq>0 (or user-defined if higher) (default: 0)
=====================================
base.cpp
=====================================
@@ -16,7 +16,7 @@ using namespace std;
typedef uint32_t DepthType; // type for depth of coverage, kept it small
const char ref_char = '>'; // reference prefix for "counts" output
-const string VERSION = "%prog 1.1.4"
+const string VERSION = "%prog 1.2.0"
"\nCopyright (C) 2014-2019 Giovanni Birolo and Andrea Telatin\n"
"https://github.com/telatin/covtobed - License MIT"
".\n"
@@ -192,6 +192,7 @@ int main(int argc, char *argv[]) {
parser.add_option("-m", "--min-cov").metavar("MINCOV").type("int").set_default("0").help("print BED feature only if the coverage is bigger than (or equal to) MINCOV (default: %default)");
parser.add_option("-x", "--max-cov").metavar("MAXCOV").type("int").set_default("100000").help("print BED feature only if the coverage is lower than MAXCOV (default: %default)");
parser.add_option("-l", "--min-len").metavar("MINLEN").type("int").set_default("1").help("print BED feature only if its length is bigger (or equal to) than MINLELN (default: %default)");
+ parser.add_option("-z", "--min-ctg-len").metavar("MINCTGLEN").type("int").help("Skip reference sequences (contigs) shorter than this value");
parser.add_option("-d", "--discard-invalid-alignments").action("store_true").set_default("0").help("skip duplicates, failed QC, and non primary alignment, minq>0 (or user-defined if higher) (default: %default)");
@@ -208,6 +209,7 @@ int main(int argc, char *argv[]) {
const int minimum_coverage = options.get("min_cov");
const int maximum_coverage = options.get("max_cov");
const int minimum_length = options.get("min_len");
+ const int minimum_contig_len= options.get("min_ctg_len");
int min_mapq = options.get("min_mapq");
if (only_valid and !min_mapq) {
@@ -232,6 +234,9 @@ int main(int argc, char *argv[]) {
for (const auto &ref : input.get_ref_data()) { // loop on reference
// init new reference data
const int ref_id = input.get_ref_id(ref.RefName);
+ if (ref.RefLength <= minimum_contig_len) {
+ continue;
+ }
debug cerr << "[R] Reference: " << ref_id << endl;
PositionType last_pos = 0;
priority_queue<CovEnd> coverage_ends;
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+covtobed (1.2.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Mon, 26 Oct 2020 02:15:17 +0530
+
covtobed (1.1.4+dfsg-2) unstable; urgency=medium
* Fix FTCBFS: Let dpkg's buildtools.mk setup cross tools (Closes: #970829)
=====================================
debian/control
=====================================
@@ -1,6 +1,6 @@
Source: covtobed
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Shayan Doust <hello at shayandoust.me>
+Uploaders: Shayan Doust <hello at shayandoust.me>, Nilesh Patra <npatra974 at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/ad6b0ebabd47531de0c82c5d2719bafaa631823f...eb142ae7778fae4af2b16cd2e29a00a579a1b215
--
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/ad6b0ebabd47531de0c82c5d2719bafaa631823f...eb142ae7778fae4af2b16cd2e29a00a579a1b215
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/20201025/532093a9/attachment-0001.html>
More information about the debian-med-commit
mailing list