[med-svn] [Git][med-team/covtobed][master] 4 commits: New upstream version 1.3.1+dfsg

Nilesh Patra (@nilesh) gitlab at salsa.debian.org
Wed Nov 3 16:03:12 GMT 2021 


Nilesh Patra pushed to branch master at Debian Med / covtobed


Commits:
15f7e4d4 by Nilesh Patra at 2021-11-03T21:01:28+05:30
New upstream version 1.3.1+dfsg
- - - - -
8bc99d60 by Nilesh Patra at 2021-11-03T21:01:59+05:30
Update upstream source from tag 'upstream/1.3.1+dfsg'

Update to upstream version '1.3.1+dfsg'
with Debian dir 14897f31f1c6667383ab680c7675149c5142bb68
- - - - -
45e38c41 by Nilesh Patra at 2021-11-03T21:22:28+05:30
Refresh patch

- - - - -
5b871a55 by Nilesh Patra at 2021-11-03T21:22:28+05:30
Upload to unstable

- - - - -


10 changed files:

- + .github/workflows/c-cpp.yml
- − .travis.yml
- README.md
- base.cpp
- debian/changelog
- debian/patches/test_use_system_installed_binary.patch
- + test/filt.bam
- + test/nano.bam
- + test/stranded.bam
- test/test.sh


Changes:

=====================================
.github/workflows/c-cpp.yml
=====================================
@@ -0,0 +1,31 @@
+name: covtobed
+'on':
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+jobs:
+  Build:
+    runs-on: '${{ matrix.os }}'
+    strategy:
+      matrix:
+        os:
+          - ubuntu-18.04
+    steps:
+      - name: Install dependencies (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |-
+          sudo apt-get update
+          sudo apt-get install -y clang-3.9 g++-6 libbamtools-dev
+      - uses: actions/checkout at v2
+      - run: '[ $CXX = g++ ] && export CXX=g++-6 || true'
+      - run: '[ $CXX = clang++ ] && export CXX=clang++-3.9 || true'
+      - run: >-
+          g++ -std=c++11 *.cpp -I/usr/include/bamtools
+          /usr/lib/x86_64-linux-gnu/libbamtools.a  -o covtobed -lz
+      - run: ./covtobed -h
+      - run: ./covtobed test/demo.bam > /dev/null
+      - run: ./covtobed --physical-coverage test/mp.bam > /dev/null
+      - run: bash test/test.sh


=====================================
.travis.yml deleted
=====================================
@@ -1,22 +0,0 @@
-language: cpp
-compiler:
-  - gcc
-  - clang
-addons:
-  apt:
-    sources:
-    - ubuntu-toolchain-r-test
-    - llvm-toolchain-precise-3.8
-    packages:
-    - g++-6
-    - clang-3.8
-    - libbamtools-dev
-install:
-- "[ $CXX = g++ ] && export CXX=g++-6 || true"
-- "[ $CXX = clang++ ] && export CXX=clang++-3.8 || true"
-script:
-  - $CXX -std=c++11 *.cpp -I/usr/include/bamtools /usr/lib/x86_64-linux-gnu/libbamtools.a  -o covtobed -lz
-  - ./covtobed -h
-  - ./covtobed test/demo.bam > /dev/null
-  - ./covtobed --physical-coverage test/mp.bam > /dev/null
-  - bash test/test.sh


=====================================
README.md
=====================================
@@ -3,8 +3,7 @@
 
 [![install with bioconda](https://img.shields.io/conda/vn/bioconda/covtobed?label=install%20from%20bioconda)](http://bioconda.github.io/recipes/covtobed/README.html)
 [![Bioconda installs](https://img.shields.io/conda/dn/bioconda/covtobed)](https://anaconda.org/bioconda/covtobed)
-[![TravisCI Build Status](https://travis-ci.org/telatin/covtobed.svg?branch=master)](https://travis-ci.org/telatin/covtobed)
-[![Docker build](https://img.shields.io/docker/pulls/andreatelatin/covtobed)](https://hub.docker.com/r/andreatelatin/covtobed)
+[![covtobed](https://github.com/telatin/covtobed/actions/workflows/c-cpp.yml/badge.svg)](https://github.com/telatin/covtobed/actions/workflows/c-cpp.yml)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/36944efb0d2b44cca850964e96c036a4)](https://www.codacy.com/manual/telatin/covtobed?utm_source=github.com&utm_medium=referral&utm_content=telatin/covtobed&utm_campaign=Badge_Grade)
 
 [![status](https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b/status.svg)](https://joss.theoj.org/papers/0ed74df9f40a58a852bf3fff512acd2b)
@@ -15,7 +14,7 @@
 Reads one (or more) [alignment](https://en.wikipedia.org/wiki/Sequence_alignment) files
 (sorted [BAM](https://en.wikipedia.org/wiki/SAM_(file_format))) and prints a [BED](https://en.wikipedia.org/wiki/BED_(file_format)) with the [coverage](https://en.wikipedia.org/wiki/Coverage_(genetics)). It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. 
 
-:book: **[Read more in the wiki](https://github.com/telatin/covtobed/wiki)** - this is the **main** documentation source
+: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`)
@@ -101,6 +100,12 @@ sudo docker run --rm -ti andreatelatin/covtobed coverage -h
 singularity exec covtobed.simg coverage -h
 ```
 
+## Startup message
+
+When invoked without arguments, covtobed will print a message to inform the user that it
+is waiting for input from STDIN.
+To suppress this message, set the environment variable `COVTOBED_QUIET` to `1`.
+
 ## Performance
 
 *covtobed* is generally faster than *bedtools*. More details are in the [benchmark](benchmark) page.
@@ -132,7 +137,7 @@ This program was finalized with a Flexible Talent Mobility Award funded by BBSRC
 
 ## Citation
 
-If you use this tool, why not citing the paper?
+If you use this tool, we would really appreciate if you will cite its paper:
 
 > Birolo et al., (2020). covtobed: a simple and fast tool to extract coverage tracks from BAM files. Journal of Open Source Software, 5(47), 2119, https://doi.org/10.21105/joss.02119
 


=====================================
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 1.2.0"
+const string VERSION = "%prog 1.3.1"
 	"\nCopyright (C) 2014-2019 Giovanni Birolo and Andrea Telatin\n"
 	"https://github.com/telatin/covtobed - License MIT"
 	".\n"
@@ -45,7 +45,12 @@ class Input {
 		Input(const vector<string> &paths, const int q, const int v) : min_mapq(q), discard_invalid_alignments(v) {
 			if (paths.empty()) {
 				// no input files, use standard input
-				cerr << "Reading from STDIN... [try 'covtobed -h' for options]" << endl;
+				// 1.3.0 - provide feedback unless $COVTOBED_QUIET is set to 1
+				// Check environment variable COVTOBED_QUIET
+				if (getenv("COVTOBED_QUIET") == NULL) {
+					cerr << "Reading from STDIN... [Ctrl+C to exit; 'covtobed -h' for help]" << endl;
+				}
+				
 				if (!input_bams.OpenFile("-"))
 					throw string("cannot read BAM from standard input, are you piping a BAM file?");
 					//throw input_bams.GetErrorString();
@@ -100,6 +105,12 @@ struct Coverage {
 		else
 			--f;
 	}
+	bool equal(const Coverage &o, bool stranded) const {
+	    	if (stranded)
+		    return f == o.f && r == o.r;
+		else
+		    return f + r == o.f + o.r;
+	}
 };
 
 // Class for output handling: writes coverage in the specified format
@@ -114,7 +125,7 @@ class Output {
 		// write interval to bed
 		void operator() (const Interval &i, const Coverage &c) {
 			// can the last interval be extended with the same coverage?
-			if (i.ref == last_interval.ref && i.start == last_interval.end && last_coverage == c)
+			if (i.ref == last_interval.ref && i.start == last_interval.end && last_coverage.equal(c, strands))
 				// extend previous interval
 				last_interval.end = i.end;
 			else {


=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+covtobed (1.3.1+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 1.3.1+dfsg
+  * Refresh patch
+
+ -- Nilesh Patra <nilesh at debian.org>  Wed, 03 Nov 2021 21:09:46 +0530
+
 covtobed (1.2.0+dfsg-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/test_use_system_installed_binary.patch
=====================================
@@ -1,10 +1,6 @@
-Description: modify test script so it works with autopkgtest
-Author: Shayan Doust <hello at shayandoust.me>
-Last-Update: 2020-06-04
----
---- covtobed.orig/test/test.sh
-+++ covtobed/test/test.sh
-@@ -7,40 +7,20 @@
+--- a/test/test.sh
++++ b/test/test.sh
+@@ -7,38 +7,18 @@
  #           ./test/mock.bam
  
  REMOVE=0
@@ -21,116 +17,137 @@ Last-Update: 2020-06-04
 -	if [ `uname` == 'Darwin' ]; then
 -		echo " - Copying macOS binary"  || echo " ERROR: pre-compiled binary not working"
 -		cp ./binaries/covtobed_mac ./covtobed
--		covtobed --version
+-		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
 -	else
 -		echo " - Trying Ubuntu binary"
 -		cp ./binaries/covtobed ./covtobed
--		covtobed --version || echo " ERROR: pre-compiled binary not working"
+-		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
 -	fi
 -fi
  
 -./covtobed --version
 +covtobed --version
  
+ echo " ================================================ "
  set -eou pipefail
  # Compilation success, checking that --version emits the expected "progname" string
  echo -n " - Compiled binary prints version: "
--if [ $(./covtobed --version  | grep covtobed | wc -l ) -eq "1" ];
-+if [ $(covtobed --version  | grep covtobed | wc -l ) -eq "1" ];
+-if [ $(./covtobed --version  | grep covtobed | wc -l ) -gt "1" ];
++if [ $(covtobed --version  | grep covtobed | wc -l ) -gt "1" ];
  then
-         echo PASS 1
+-        echo PASS $(./covtobed --version | grep covtobed |head -n 1)
++        echo PASS $(covtobed --version | grep covtobed |head -n 1)
+ else
+-        echo FAIL $(./covtobed --version  | grep covtobed | wc -l )
++        echo FAIL $(covtobed --version  | grep covtobed | wc -l )
+ 		exit
  fi
  
+@@ -46,7 +26,7 @@
+ 
  # Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)
  echo -n " - Minimum coverage, expected BED lines check: "
 -if [ $(./covtobed -m 15 test/demo.bam  | wc -l) -eq "12" ];
-+if [ $(covtobed -m 15 /usr/share/doc/covtobed-examples/examples/demo.bam  | wc -l) -eq "12" ];
++if [ $(covtobed -m 15 demo.bam  | wc -l) -eq "12" ];
  then
  	echo PASS 2
  else
-@@ -50,7 +30,7 @@
+@@ -56,7 +36,7 @@
  
  # Checking thath --physical-coverage will work, and it fits the expected number of lines
  echo -n " - Physical coverage, expected BED lines check: "
 -if [ $(./covtobed --physical-coverage test/mp.bam  | wc -l) -eq "136" ];
-+if [ $(covtobed --physical-coverage /usr/share/doc/covtobed-examples/examples/mp.bam  | wc -l) -eq "136" ];
++if [ $(covtobed --physical-coverage mp.bam  | wc -l) -eq "136" ];
  then
  	echo PASS 3
  else
-@@ -60,7 +40,7 @@
+@@ -66,7 +46,7 @@
  
  # Checking stranded output: it should produce content in the fifth column of the bed file
  echo -n " - Stranded output, testing column #5: "
 -if [ $(./covtobed --out test/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];
-+if [ $(covtobed --out /usr/share/doc/covtobed-examples/examples/demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];
++if [ $(covtobed --out demo.bam | cut -f 5 | sort -u | wc -l) -eq "10" ];
  then
  	echo PASS 4
  else
-@@ -70,7 +50,7 @@
+@@ -76,7 +56,7 @@
  
  # Checking the "counts" output (counting the lines containing a ">")
  echo -n " - Testing 'counts' format (printed headers): "
 -if [ $(./covtobed --format counts test/demo.bam | grep '>' | wc -l) -eq "2" ];
-+if [ $(covtobed --format counts /usr/share/doc/covtobed-examples/examples/demo.bam | grep '>' | wc -l) -eq "2" ];
++if [ $(covtobed --format counts demo.bam | grep '>' | wc -l) -eq "2" ];
  then
  	echo PASS 5
  else
-@@ -78,7 +58,7 @@
+@@ -84,29 +64,29 @@
  	exit 1
  fi
  echo -n " - Testing 'counts' format (printed lines): "
--if [ $(./covtobed --format counts test/demo.bam | grep -v '>' | wc -l) -eq "202" ];
-+if [ $(covtobed --format counts /usr/share/doc/covtobed-examples/examples/demo.bam | grep -v '>' | wc -l) -eq "202" ];
+-if [ $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) -eq "202" ];
++if [ $(covtobed --format counts demo.bam | grep -v \> | wc -l) -eq "202" ];
  then
          echo PASS 6
  else
-@@ -88,11 +68,11 @@
+-	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
++	echo FAIL $(covtobed --format counts demo.bam | grep -v \> | wc -l) when 202 expected
+ 	exit 1
+ fi
  
+ echo -n " - Testing strand with adjacent intervals: "
+-if [[ $(./covtobed  test/stranded.bam | wc -l) -eq "1"  && $(./covtobed --output-strands test/stranded.bam | wc -l) -eq "2" ]];
++if [[ $(covtobed  stranded.bam | wc -l) -eq "1"  && $(covtobed --output-strands stranded.bam | wc -l) -eq "2" ]];
+ then
+         echo PASS 7
+ else
+-	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
++	echo FAIL $(covtobed --format counts demo.bam | grep -v \> | wc -l) when 202 expected
+ 	exit 1
+ fi
  # Checking BED output with reference output file
  echo -n " - Checking identity of BED output with pre-calculated: "
 -./covtobed test/demo.bam > test/output.test
 -if [ $(diff test/output.test test/output.bed | wc -l) -eq "0" ];
-+covtobed /usr/share/doc/covtobed-examples/examples/demo.bam > output.test
-+if [ $(diff output.test /usr/share/doc/covtobed-examples/examples/output.bed | wc -l) -eq "0" ];
++covtobed demo.bam > output.test
++if [ $(diff output.test output.bed | wc -l) -eq "0" ];
  then
-         echo PASS 7
+         echo PASS 8
 -	rm test/output.test
 +	rm output.test
  else
  	echo FAIL
  	exit 1
-@@ -100,11 +80,11 @@
+@@ -114,11 +94,11 @@
  
  ## Synthetic BAM test
  echo -n " - Checking computed coverage for a synthetic BAM file: "
 -./covtobed -m 1 test/mock.bam > test/output.test
 -if [ $(diff test/output.test test/mock.bed | wc -l) -eq "0" ];
-+covtobed -m 1 /usr/share/doc/covtobed-examples/examples/mock.bam > output.test
-+if [ $(diff output.test /usr/share/doc/covtobed-examples/examples/mock.bed | wc -l) -eq "0" ];
++covtobed -m 1 mock.bam > output.test
++if [ $(diff output.test mock.bed | wc -l) -eq "0" ];
  then
-         echo PASS 8
+         echo PASS 9
 -	rm test/output.test
 +	rm output.test
  else
  	echo FAIL
  	exit 1
-@@ -112,23 +92,23 @@
+@@ -126,23 +106,23 @@
  
  ## Filter non valid alignments
  echo -n " - Checking filtering of invalid alignments: "
 -if [ $(./covtobed -m 1 -d test/filtered.bam | wc -l) -eq "2" ] ; then
-+if [ $(covtobed -m 1 -d /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l) -eq "2" ] ; then
- 	echo -n "PASS 9,"
++if [ $(covtobed -m 1 -d filtered.bam | wc -l) -eq "2" ] ; then
+ 	echo -n "PASS 10,"
  else
  	echo FAIL
  	exit 1
  fi
 -if [ $(./covtobed -m 1 test/filtered.bam | wc -l) -eq "6" ] ; then
-+if [ $(covtobed -m 1 /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l) -eq "6" ] ; then
++if [ $(covtobed -m 1 filtered.bam | wc -l) -eq "6" ] ; then
  	echo 10
  else
 -	echo "FAIL: $(./covtobed -m 1 -d test/filtered.bam | wc -l)"
-+	echo "FAIL: $(covtobed -m 1 -d /usr/share/doc/covtobed-examples/examples/filtered.bam | wc -l)"
++	echo "FAIL: $(covtobed -m 1 -d filtered.bam | wc -l)"
  	exit 1
  fi
  
@@ -138,15 +155,14 @@ Last-Update: 2020-06-04
  # covered exactly {n}X times
  echo  " - Checking artificial coverage values:"
 -./covtobed test/test_cov.bam -m 1 |cut -f 1,4| while read LINE;
-+covtobed /usr/share/doc/covtobed-examples/examples/test_cov.bam -m 1 |cut -f 1,4| while read LINE;
++covtobed test_cov.bam -m 1 |cut -f 1,4| while read LINE;
  do
  	echo "$LINE" | perl -ne '($exp, $cov)=split /\s+/, $_; if ("$exp" ne "${cov}X") {
  		die "$exp != $cov\n";
-@@ -137,7 +117,3 @@
- 	}'
- done
+@@ -153,5 +133,5 @@
  echo "ALL TESTS: PASSED"
--
--if [[ $REMOVE -eq 1 ]]; then
+ 
+ if [[ $REMOVE -eq 1 ]]; then
 - rm ./covtobed
--fi
++ rm covtobed
+ fi


=====================================
test/filt.bam
=====================================
Binary files /dev/null and b/test/filt.bam differ


=====================================
test/nano.bam
=====================================
Binary files /dev/null and b/test/nano.bam differ


=====================================
test/stranded.bam
=====================================
Binary files /dev/null and b/test/stranded.bam differ


=====================================
test/test.sh
=====================================
@@ -20,24 +20,30 @@ if [ ! -e "./covtobed" ]; then
 	if [ `uname` == 'Darwin' ]; then
 		echo " - Copying macOS binary"  || echo " ERROR: pre-compiled binary not working"
 		cp ./binaries/covtobed_mac ./covtobed
-		covtobed --version
+		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
 	else
 		echo " - Trying Ubuntu binary"
 		cp ./binaries/covtobed ./covtobed
-		covtobed --version || echo " ERROR: pre-compiled binary not working"
+		covtobed --version >/dev/null || echo " ERROR: pre-compiled binary not working"
 	fi
 fi
 
 ./covtobed --version
 
+echo " ================================================ "
 set -eou pipefail
 # Compilation success, checking that --version emits the expected "progname" string
 echo -n " - Compiled binary prints version: "
-if [ $(./covtobed --version  | grep covtobed | wc -l ) -eq "1" ];
+if [ $(./covtobed --version  | grep covtobed | wc -l ) -gt "1" ];
 then
-        echo PASS 1
+        echo PASS $(./covtobed --version | grep covtobed |head -n 1)
+else
+        echo FAIL $(./covtobed --version  | grep covtobed | wc -l )
+		exit
 fi
 
+
+
 # Testing that -m MIN produces an output, and it fits the expectation for demo.bam (n. lines)
 echo -n " - Minimum coverage, expected BED lines check: "
 if [ $(./covtobed -m 15 test/demo.bam  | wc -l) -eq "12" ];
@@ -78,20 +84,28 @@ else
 	exit 1
 fi
 echo -n " - Testing 'counts' format (printed lines): "
-if [ $(./covtobed --format counts test/demo.bam | grep -v '>' | wc -l) -eq "202" ];
+if [ $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) -eq "202" ];
 then
         echo PASS 6
 else
-	echo FAIL
+	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
 	exit 1
 fi
 
+echo -n " - Testing strand with adjacent intervals: "
+if [[ $(./covtobed  test/stranded.bam | wc -l) -eq "1"  && $(./covtobed --output-strands test/stranded.bam | wc -l) -eq "2" ]];
+then
+        echo PASS 7
+else
+	echo FAIL $(./covtobed --format counts test/demo.bam | grep -v \> | wc -l) when 202 expected
+	exit 1
+fi
 # Checking BED output with reference output file
 echo -n " - Checking identity of BED output with pre-calculated: "
 ./covtobed test/demo.bam > test/output.test
 if [ $(diff test/output.test test/output.bed | wc -l) -eq "0" ];
 then
-        echo PASS 7
+        echo PASS 8
 	rm test/output.test
 else
 	echo FAIL
@@ -103,7 +117,7 @@ echo -n " - Checking computed coverage for a synthetic BAM file: "
 ./covtobed -m 1 test/mock.bam > test/output.test
 if [ $(diff test/output.test test/mock.bed | wc -l) -eq "0" ];
 then
-        echo PASS 8
+        echo PASS 9
 	rm test/output.test
 else
 	echo FAIL
@@ -113,7 +127,7 @@ fi
 ## Filter non valid alignments
 echo -n " - Checking filtering of invalid alignments: "
 if [ $(./covtobed -m 1 -d test/filtered.bam | wc -l) -eq "2" ] ; then
-	echo -n "PASS 9,"
+	echo -n "PASS 10,"
 else
 	echo FAIL
 	exit 1



View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957

-- 
View it on GitLab: https://salsa.debian.org/med-team/covtobed/-/compare/761ae720607b2c255cd10ec51448d34f2e13f3c3...5b871a5527ac9f9b0e8c5010b14a62e21b930957
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