[med-svn] [Git][med-team/mosdepth][upstream] New upstream version 0.3.2+ds
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Oct 6 15:53:13 BST 2021
Andreas Tille pushed to branch upstream at Debian Med / mosdepth
Commits:
7fc352ea by Andreas Tille at 2021-10-06T16:47:56+02:00
New upstream version 0.3.2+ds
- - - - -
5 changed files:
- .github/workflows/build.yml
- README.md
- mosdepth.nim
- mosdepth.nimble
- scripts/install.sh
Changes:
=====================================
.github/workflows/build.yml
=====================================
@@ -50,26 +50,27 @@ jobs:
sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
-
- - name: Install d4
- git clone https://github.com/38/d4-format
- cd d4-format
- cargo build --release
- sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib
- sudo cp ./d4binding/include/d4.h /usr/local/include/
-
# Setup htslib
- name: Install htslib (linux)
if: runner.os == 'Linux'
run: |
cd
git clone --recursive https://github.com/samtools/htslib.git
- cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
+ cd htslib && git checkout 1.11 && autoheader && autoconf && ./configure --enable-libcurl
cd
- make -j 4 -C htslib
+ make -j 4 -C htslib install
echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
ls -lh $HOME/htslib/*.so
+ - name: Install d4
+ export HTSLIB=system
+ git clone https://github.com/38/d4-format
+ cd d4-format
+ cargo build --release
+ sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib
+ sudo cp ./d4binding/include/d4.h /usr/local/include/
+
+
- name: Install hstlib (macos)
if: runner.os == 'macOS'
run: |
=====================================
README.md
=====================================
@@ -63,6 +63,7 @@ Other options:
-T --thresholds <thresholds> for each interval in --by, write number of bases covered by at
least threshold bases. Specify multiple integer values separated
by ','.
+ -m --use-median output median of each region (in --by) instead of mean.
-R --read-groups <string> only calculate depth for these comma-separated read groups IDs.
-h --help show help
@@ -207,7 +208,7 @@ close to 30X coverage for almost 40% of the genome.
-See [this blog post](http://www.gettinggeneticsdone.com/2014/03/visualize-coverage-exome-targeted-ngs-bedtools.html) for
+See [this blog post](https://web.archive.org/web/20181018084459/http://www.gettinggeneticsdone.com/2014/03/visualize-coverage-exome-targeted-ngs-bedtools.html) for
more details.
## thresholds
=====================================
mosdepth.nim
=====================================
@@ -229,7 +229,7 @@ proc init(arr: var coverage_t, tlen:int) =
arr.set_len(int(tlen))
zeroMem(arr[0].addr, len(arr) * sizeof(arr[0]))
-proc coverage(bam: hts.Bam, arr: var coverage_t, region: var region_t, mapq:int= -1, eflag: uint16=1796, iflag:uint16=0, read_groups:seq[cstring]=(@[]), fast_mode:bool=false): int =
+proc coverage(bam: hts.Bam, arr: var coverage_t, region: var region_t, mapq:int= -1, eflag: uint16=1796, iflag:uint16=0, read_groups:seq[string]=(@[]), fast_mode:bool=false): int =
# depth updates arr in-place and yields the tid for each chrom.
# returns -1 if the chrom is not found in the bam header
# returns -2 if the chrom was found in the header, but there was no data for it
@@ -258,7 +258,7 @@ proc coverage(bam: hts.Bam, arr: var coverage_t, region: var region_t, mapq:int=
if iflag != 0 and ((rec.flag and iflag) == 0):
continue
if has_read_groups:
- var t = tag[cstring](rec, "RG")
+ var t = tag[string](rec, "RG")
if t.isNone or not read_groups.contains(t.get):
continue
if tgt.tid != rec.b.core.tid:
@@ -551,7 +551,7 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16
var
targets = bam.hdr.targets
sub_targets = get_targets(targets, chrom)
- read_groups: seq[cstring]
+ read_groups: seq[string]
rchrom : region_t
arr: coverage_t
prefix: string = $(args["<prefix>"])
@@ -582,7 +582,7 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, eflag: uint16, iflag: uint16
if $args["--read-groups"] != "nil":
for r in ($args["--read-groups"]).split(','):
- read_groups.add(r.cstring)
+ read_groups.add($r)
var levels = get_min_levels(targets)
var chrom_region_distribution, chrom_global_distribution: seq[int64]
@@ -775,7 +775,7 @@ when(isMainModule):
when not defined(release) and not defined(lto):
stderr.write_line "[mosdepth] WARNING: built in debug mode; will be slow"
- let version = "mosdepth 0.3.1"
+ let version = "mosdepth 0.3.2"
let env_fasta = getEnv("REF_PATH")
var doc = format("""
$version
@@ -845,7 +845,7 @@ Other options:
region = $args["--by"]
else:
if thresholds.len != 0:
- stderr.write_line("[mosdepth] error --thresholds can noly be used when --by is specified.")
+ stderr.write_line("[mosdepth] error --thresholds can only be used when --by is specified.")
quit(2)
GC_disableMarkAndSweep()
var fasta: cstring = nil
=====================================
mosdepth.nimble
=====================================
@@ -1,6 +1,6 @@
# Package
-version = "0.3.1"
+version = "0.3.2"
author = "Brent Pedersen"
description = "fast depth"
license = "MIT"
=====================================
scripts/install.sh
=====================================
@@ -23,16 +23,17 @@ $base/nim-$BRANCH/bin/nimble install -y
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -qy
-export HTSLIB=dynamic
+export HTSLIB=system
sudo apt-get update
sudo apt-get install git llvm curl wget libcurl4-openssl-dev
-wget https://github.com/samtools/htslib/archive/1.10.2.tar.gz
-tar xzf 1.10.2.tar.gz
-cd htslib-1.10.2/
-autoheader && autoconf && ./configure --enable-libcurl
+wget https://github.com/samtools/htslib/archive/1.11.tar.gz
+tar xzf 1.11.tar.gz
+cd htslib-1.11/
+autoheader && autoconf && ./configure --disable-libcurl
sudo make -j4 install
git clone https://github.com/38/d4-format
cd d4-format
+
~/.cargo/bin/cargo build --release
sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib
sudo cp ./d4binding/include/d4.h /usr/local/include/
View it on GitLab: https://salsa.debian.org/med-team/mosdepth/-/commit/7fc352ea0169927715382ecc0833f75d4ec81653
--
View it on GitLab: https://salsa.debian.org/med-team/mosdepth/-/commit/7fc352ea0169927715382ecc0833f75d4ec81653
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