[med-svn] [Git][med-team/nim-hts][master] 7 commits: Fix watchfile to detect new versions on github
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Oct 12 06:52:40 BST 2021
Andreas Tille pushed to branch master at Debian Med / nim-hts
Commits:
350fe2df by Andreas Tille at 2021-10-12T07:43:27+02:00
Fix watchfile to detect new versions on github
- - - - -
6f357a96 by Andreas Tille at 2021-10-12T07:43:30+02:00
New upstream version 0.3.18+ds
- - - - -
24642194 by Andreas Tille at 2021-10-12T07:43:30+02:00
routine-update: New upstream version
- - - - -
69939d33 by Andreas Tille at 2021-10-12T07:43:31+02:00
Update upstream source from tag 'upstream/0.3.18+ds'
Update to upstream version '0.3.18+ds'
with Debian dir 48f8d56500a4dc1598faddbc24c311b79863055a
- - - - -
0a8d3003 by Andreas Tille at 2021-10-12T07:43:31+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
5f49d6f3 by Andreas Tille at 2021-10-12T07:43:38+02:00
Apply multi-arch hints.
+ nim-hts-examples: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
b7b62b80 by Andreas Tille at 2021-10-12T07:44:35+02:00
routine-update: Ready to upload to unstable
- - - - -
15 changed files:
- CHANGES.md
- Dockerfile
- README.md
- debian/changelog
- debian/control
- debian/watch
- docker/docker.nim.cfg
- hts.nimble
- src/hts/bam.nim
- src/hts/private/hts_concat.h
- src/hts/private/hts_concat.nim
- src/hts/vcf.nim
- tests/test_readme.nim
- + tests/test_same_header.vcf.gz
- tests/vcftest.nim
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,3 +1,20 @@
+v0.3.18
+=======
++ [vcf] fix for #77 for to avoid double-free of header when it's re-used.
+
+v0.3.17
+=======
++ turn quits into exceptions
+
+v0.3.16
+=======
++ expose VCF.fname
++ change rendering of unknown alleles to fix './.'
+
+v0.3.15
+=======
++ vcf: expose a couple more functions from htslib
+
v0.3.14
=======
+ add close method to fai for consistency (continues to also occur automatically upon garbage collection) #70
=====================================
Dockerfile
=====================================
@@ -4,7 +4,7 @@ FROM alpine:3.11.5
ENV CFLAGS="-fPIC -O3"
RUN apk add wget git xz bzip2-static musl m4 autoconf tar xz-dev bzip2-dev build-base libpthread-stubs libzip-dev gfortran \
- openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static bash
+ openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static bash curl-dev clang-static nghttp2-static
RUN mkdir -p /usr/local/include && \
git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
@@ -15,8 +15,9 @@ RUN mkdir -p /usr/local/include && \
cd .. && \
rm -rf cloudflare-zlib
+
RUN cd / && \
- git clone -b v1.2.6 git://github.com/nim-lang/nim nim && \
+ git clone -b v1.4.8 git://github.com/nim-lang/nim nim && \
cd nim && \
sh ./build_all.sh && \
rm -rf csources && \
@@ -37,14 +38,14 @@ RUN apk add cmake openssl-dev && \
ENV PATH=:/root/.nimble/bin:/nim/bin/:$PATH
RUN \
- git clone https://github.com/samtools/htslib && \
- cd htslib && git checkout 1.11 && autoheader && autoconf && \
- ./configure --disable-s3 --disable-libcurl --with-libdeflate && \
+ git clone -b 1.13 --recursive https://github.com/samtools/htslib && \
+ cd htslib && autoheader && autoconf && \
+ ./configure --enable-s3 --enable-libcurl --with-libdeflate && \
make -j4 CFLAGS="-fPIC -O3" install && \
cd ../ && \
- git clone https://github.com/samtools/bcftools && \
- cd bcftools && git checkout 1.10.2 && autoheader && autoconf && \
- ./configure --disable-s3 --disable-libcurl --with-libdeflate && \
+ git clone -b 1.13 --recursive https://github.com/samtools/bcftools && \
+ cd bcftools && autoheader && autoconf && \
+ ./configure --enable-s3 --enable-libcurl --with-libdeflate && \
make -j4 CFLAGS="-fPIC -O3" install && \
cd ../ && rm -rf htslib bcftools
@@ -52,10 +53,8 @@ RUN \
RUN sh -c 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -q -y'
# && apk add clang-libs
-ENV HTSLIB=system
ENV PATH=$PATH:~/.cargo/bin/
-
-#COPY docker/d4.patch /tmp/
+ENV RUSTFLAGS=-Ctarget-feature=-crt-static
#&& git apply < /tmp/d4.patch \
RUN ~/.cargo/bin/rustup target add x86_64-unknown-linux-musl \
=====================================
README.md
=====================================
@@ -176,3 +176,19 @@ At this time, libcurl is not supported so only binaries built using this method
The docker images does use [libdeflate](https://github.com/ebiggers/libdeflate) by default. That provides,
for example, a 20% speed improvement when used to build [mosdepth](https://github.com/brentp/mosdepth).
+
+### Static binary with singularity
+
+The default static build setup uses docker on linux. This is not possible on some clusters. To build a project using singularity, use something like this:
+
+```
+singularity run \
+ --bind $(pwd):/load \
+ --bind /scratch \
+ --bind /uufs \
+ 'docker://brentp/musl-hts-nim:latest' /usr/local/bin/nsb -n slivar.nimble -s src/slivar.nim -- -d:danger -d:release
+```
+where the first `bind` is required as-is. The other binds can be modified to adjust which paths on the machine need to be available to access all
+local source files. This command will create a `slivar` executable in `pwd`.
+Then, replace `slivar.nimble` with your nimble file and `src/slivar.nim` with your main source file.
+It's also sometimes useful to replace `-d:danger -d:release` with `-d:debug` to get a debug build.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+nim-hts (0.3.18+ds-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Oct 2021 07:43:40 +0200
+
+nim-hts (0.3.14+ds-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Fix watchfile to detect new versions on github
+
+ -- Andreas Tille <tille at debian.org> Tue, 12 Oct 2021 07:43:27 +0200
+
nim-hts (0.3.14+ds-2) unstable; urgency=medium
* d/p/fix-version-comparision.patch: Fix version comparison
=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
samtools,
tabix,
bcftools
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Homepage: https://github.com/brentp/hts-nim
Vcs-Browser: https://salsa.debian.org/med-team/nim-hts
Vcs-Git: https://salsa.debian.org/med-team/nim-hts.git
@@ -31,6 +31,7 @@ Package: nim-hts-examples
Architecture: all
Depends: ${misc:Depends}
Enhances: nim-hts-dev
+Multi-Arch: foreign
Description: examples for nim-hts: wrapper for hts C library
The hts library is well accepted for the handling of millions of
DNA sequences from what once was the high-throughput sequencing machines
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \
-https://github.com/brentp/hts-nim/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
+https://github.com/brentp/hts-nim/releases .*/v?@ANY_VERSION@\.tar\.gz
=====================================
docker/docker.nim.cfg
=====================================
@@ -4,8 +4,9 @@
passC:"-static"
#define:"lapack=openblas"
# define:"blas=openblas"
- passl:"-static -no-pie -fno-pie"
+ passl:"-static -no-pie -fno-pie -Wl,--start-group"
passl:"/usr/lib/libm.a"
+ passl:"/usr/lib/libcurl.a"
passl:"/usr/local/lib/libhts.a"
passl:"/usr/local/lib/libdeflate.a"
passl:"/usr/local/lib/libz.a"
@@ -24,10 +25,8 @@
passl:"/usr/lib/libc.a"
passl:"/usr/lib/librt.a"
passl:"/usr/lib/libpcre.a"
- passl:"/usr/lib/libd4binding.a"
-# passl:"/usr/local/lib/libnghttp2.a"
-# passl:"/usr/lib/libcurl.a"
+ passl:"/usr/lib/libnghttp2.a"
# passl:"/usr/local/lib/libnghttp2.a"
# passl:"/usr/lib/libcurl.a"
=====================================
hts.nimble
=====================================
@@ -1,6 +1,6 @@
# Package
-version = "0.3.14"
+version = "0.3.18"
author = "Brent Pedersen"
description = "hts (bam/sam) for nim"
license = "MIT"
=====================================
src/hts/bam.nim
=====================================
@@ -169,14 +169,14 @@ proc mate_chrom*(r: Record): string {.inline.} =
return ""
return $r.hdr.hdr.target_name[tid]
-proc mate_tid*(r: Record): int {.inline.} =
- ## `mate_tid` returns the tid of the mate or -1 if not mapped.
- result = r.b.core.mtid
-
proc tid*(r: Record): int {.inline.} =
## `tid` returns the tid of the alignment or -1 if not mapped.
result = r.b.core.tid
+proc mate_tid*(r: Record): int {.inline.} =
+ ## `mate_tid` returns the tid of the mate or -1 if not mapped.
+ result = r.b.core.mtid
+
proc start*(r: Record): int64 {.inline.} =
## `start` returns 0-based start position.
return r.b.core.pos
=====================================
src/hts/private/hts_concat.h
=====================================
@@ -607,6 +607,7 @@ int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...);
void bcf_hdr_remove(bcf_hdr_t *h, int type, const char *key);
int bcf_hdr_add_sample(bcf_hdr_t *hdr, const char *sample);
+bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src);
=====================================
src/hts/private/hts_concat.nim
=====================================
@@ -8,10 +8,6 @@ elif defined(macosx):
else:
const
libname* = "libhts.so"
-
-when (NimMajor, NimMinor) < (1, 1):
- type
- csize_t* = csize
##
## enum hts_fmt_option {
## // CRAM specific
@@ -719,6 +715,8 @@ proc bcf_hdr_remove*(h: ptr bcf_hdr_t; `type`: cint; key: cstring) {.cdecl,
importc: "bcf_hdr_remove", dynlib: libname.}
proc bcf_hdr_add_sample*(hdr: ptr bcf_hdr_t; sample: cstring): cint {.cdecl,
importc: "bcf_hdr_add_sample", dynlib: libname.}
+proc bcf_hdr_merge*(dst: ptr bcf_hdr_t; src: ptr bcf_hdr_t): ptr bcf_hdr_t {.cdecl,
+ importc: "bcf_hdr_merge", dynlib: libname.}
template bcf_hdr_nsamples*(hdr: untyped): untyped =
(hdr).n[BCF_DT_SAMPLE]
=====================================
src/hts/vcf.nim
=====================================
@@ -22,7 +22,7 @@ type
c: ptr bcf1_t
bidx: ptr hts_idx_t
tidx: ptr tbx_t
- fname: string
+ fname*: string
Variant* = ref object
## Variant is a single line from a VCF
@@ -187,7 +187,9 @@ proc remove_format*(h:Header, ID:string): Status =
return Status(bcf_hdr_sync(h.hdr))
proc destroy_vcf(v:VCF) =
- bcf_hdr_destroy(v.header.hdr)
+ if v.header != nil and v.header.hdr != nil:
+ bcf_hdr_destroy(v.header.hdr)
+ v.header.hdr = nil
if v.tidx != nil:
tbx_destroy(v.tidx)
if v.bidx != nil:
@@ -196,7 +198,8 @@ proc destroy_vcf(v:VCF) =
bcf_destroy(v.c)
if v.fname != "-" and v.fname != "/dev/stdin":
if v.hts != nil:
- discard hts_close(v.hts)
+ if hts_close(v.hts) != 0:
+ stderr.write_line "[hts-nim] underlying error closing vcf file"
v.hts = nil
else:
flushFile(stdout)
@@ -576,7 +579,7 @@ iterator items*(v:VCF): Variant =
if v.c.errcode > 1:
stderr.write_line "hts-nim/vcf bcf_read error:" & $v.c.errcode
stderr.write_line "last read variant:", variant.tostring()
- quit(2)
+ raise newException(IOError, "Error reading variant")
type Contig* = object
@@ -639,7 +642,7 @@ iterator vquery(v:VCF, region:string): Variant =
v.tidx = tbx_index_load(v.fname)
if v.tidx == nil:
stderr.write_line("hts-nim/vcf no index found for " & v.fname)
- quit(2)
+ raise newException(IOError, "No Index found for " & v.fname)
var
read_func:ptr hts_readrec_func = cast[ptr hts_readrec_func](tbx_readrec)
@@ -695,7 +698,7 @@ iterator query*(v:VCF, region: string): Variant =
if v.bidx == nil:
stderr.write_line("hts-nim/vcf no index found for " & v.fname)
- quit(2)
+ raise newException(IOError, "No Index found for " & v.fname)
var
start: int64
stop: int64
@@ -723,7 +726,7 @@ iterator query*(v:VCF, region: string): Variant =
hts_itr_destroy(itr)
if ret > 0:
stderr.write_line "hts-nim/vcf: error parsing "
- quit(2)
+ raise newException(IOError, "error parsing vcf")
if v.c.errcode != 0:
stderr.write_line "hts-nim/vcf bcf_read error:" & $v.c.errcode
@@ -859,7 +862,7 @@ proc `$`*(a:Allele): string {.inline.} =
## string representation of a single allele.
if a.value < 0:
# set end to / so it is removed in '$'
- result = if int32(a) == 0: "." else: "$"
+ result = if int32(a) == 0: "./" else: "$"
else:
result = intToStr(a.value) & (if a.phased: '|' else: '/')
=====================================
tests/test_readme.nim
=====================================
@@ -10,7 +10,7 @@ randomize()
proc getRandomNimname(length: int = 8): string =
result = "test_"
- for _ in ..length:
+ for _ in 0..length:
result.add(sample(IdentChars))
result.add(".nim")
=====================================
tests/test_same_header.vcf.gz
=====================================
Binary files /dev/null and b/tests/test_same_header.vcf.gz differ
=====================================
tests/vcftest.nim
=====================================
@@ -285,7 +285,7 @@ suite "vcf suite":
global_variant.ID = "rs0123456789"
check global_variant.ID == "rs0123456789"
- check global_variant.tostring.split('\t')[..2] == @["1", "10172", "rs0123456789"]
+ check global_variant.tostring.split('\t')[0..2] == @["1", "10172", "rs0123456789"]
test "new from string":
var v:VCF
@@ -400,6 +400,22 @@ suite "vcf alleles":
v.ALT = @["A", "T"]
check v.ALT == @["A", "T"]
+proc write_linked_blocks(ivcf:var VCF, ovcf:var VCF):int =
+ var current_line: string
+ var v_off = 1
+ var currentBlock = 0
+ doAssert Status.OK == ivcf.header.add_string("""##sgcocaller_v0.1=phaseBlocks""")
+ ovcf.header = ivcf.header
+ doAssert ovcf.write_header()
+ var gt_string:seq[int32]
+ var block_pos_i = 0
+ for v in ivcf.query("*"):
+ gt_string = @[int32(2),int32(5)]
+ if v.format().set("GT",gt_string) != Status.OK:
+ quit "set GT failed"
+ if not ovcf.write_variant(v) :
+ quit "write vcf failed for " & $voff
+ return 0
suite "bug suite":
test "csq reader":
@@ -411,6 +427,25 @@ suite "bug suite":
var st = variant.info.get("CSQ", anno)
check st in {Status.OK, Status.NotFound}
+ test "re-use same header issue 77":
+ let threads = 1
+ var chrs = @["chr1", "chr1"]
+
+ var ivcf,ovcf: VCF
+ var inFile,outFile:string
+
+ for chrName in chrs:
+ inFile = "tests/test_same_header.vcf.gz"
+ outFile = "__x.vcf.gz"
+ if not open(ivcf, inFile, threads=threads):
+ quit "couldn't open input vcf file"
+ if not open(ovcf, outFile, threads=threads, mode ="w"):
+ quit "couldn't open output vcf file"
+ doAssert 0 == write_linked_blocks(ivcf,ovcf)
+ ivcf.close()
+ ovcf.close()
+
+
import times
suite "speed tests":
View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/compare/ec5566514f2546ea1d403096282ca526f5e89915...b7b62b80f68aa77984216554ec76b92e77abd4d4
--
View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/compare/ec5566514f2546ea1d403096282ca526f5e89915...b7b62b80f68aa77984216554ec76b92e77abd4d4
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/20211012/300dfa0b/attachment-0001.htm>
More information about the debian-med-commit
mailing list