[med-svn] [Git][med-team/nim-hts][upstream] New upstream version 0.3.13+ds
Nilesh Patra
gitlab at salsa.debian.org
Thu Nov 26 11:56:15 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / nim-hts
Commits:
05e0b475 by Nilesh Patra at 2020-11-26T11:52:20+00:00
New upstream version 0.3.13+ds
- - - - -
6 changed files:
- CHANGES.md
- Dockerfile
- − Dockerfile.musl-hts-nim
- README.md
- src/hts/private/hts_concat.nim
- src/hts/vcf.nim
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,3 +1,7 @@
+v0.3.13
+=======
++ changes for nim ORC/ARC GCs
+
v0.3.11
=======
+ add bgzi.open which allows opening for reading and writing without quit() and replaces
=====================================
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
+ openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static bash
RUN mkdir -p /usr/local/include && \
git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
@@ -38,7 +38,7 @@ ENV PATH=:/root/.nimble/bin:/nim/bin/:$PATH
RUN \
git clone https://github.com/samtools/htslib && \
- cd htslib && git checkout 1.10.2 && autoheader && autoconf && \
+ cd htslib && git checkout 1.11 && autoheader && autoconf && \
./configure --disable-s3 --disable-libcurl --with-libdeflate && \
make -j4 CFLAGS="-fPIC -O3" install && \
cd ../ && \
@@ -49,20 +49,20 @@ RUN \
cd ../ && rm -rf htslib bcftools
+RUN sh -c 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -q -y'
+# && apk add clang-libs
-RUN sh -c 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -q -y' \
- && apk add clang-libs
-
-ENV HTSLIB=dynamic
+ENV HTSLIB=system
ENV PATH=$PATH:~/.cargo/bin/
-COPY docker/d4.patch /tmp/
+#COPY docker/d4.patch /tmp/
+#&& git apply < /tmp/d4.patch \
RUN ~/.cargo/bin/rustup target add x86_64-unknown-linux-musl \
&& git clone https://github.com/38/d4-format \
&& cd d4-format \
- && git apply < /tmp/d4.patch \
- && ~/.cargo/bin/cargo build --target x86_64-unknown-linux-musl --release
+ && ln -s /usr/bin/gcc /usr/bin/musl-gcc \
+ && ~/.cargo/bin/cargo build --all --target x86_64-unknown-linux-musl --release
RUN install -m 644 d4-format/target/x86_64-unknown-linux-musl/release/libd4binding.a /usr/lib && \
install -m 644 d4-format/d4binding/include/d4.h /usr/include
=====================================
Dockerfile.musl-hts-nim deleted
=====================================
@@ -1,38 +0,0 @@
-## This dockerfile
-# 1. builds htslib and all dependencies currently without libcurl
-# 2. installs nim
-# 3. sets up a nim binary (nsb) that is expected to be called from an external binary (static_builder)
-# These facilitate building static binaries for projects using hts-nim.
-
-# docker build -t brentp/musl-hts-nim:latest -f Dockerfile.musl-hts-nim ..
-FROM alpine:3.9
-
-ENV LDFLAGS=-static PKG_CONFIG='pkg-config --static'
-ENV curl_LDFLAGS=-all-static
-
-RUN apk add curl musl build-base git autoconf zlib-dev bzip2-dev xz-dev curl-dev
-
-RUN cd / && \
- git clone -b devel --depth 10 git://github.com/nim-lang/nim nim && \
- cd nim && sh ./build_all.sh
-
-RUN git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
- cd libdeflate && make -j 2 CFLAGS='-fPIC -O3' libdeflate.a && \
- cp libdeflate.a /usr/local/lib && cp libdeflate.h /usr/include && \
- cd .. && rm -rf libdeflate && \
- git clone https://github.com/samtools/htslib && \
- cd htslib && git checkout 1.9 && autoheader && autoconf && \
- ./configure --enable-plugins --disable-libcurl --with-libdeflate && \
- make -j4 install && \
- cd ../ && rm -rf htslib
-
-ADD . /src/
-
-ENV PATH=/root/.nimble/bin:/nim/bin/:$PATH
-
-RUN cat /src/docker/docker.nim.cfg >> /nim/config/nim.cfg && \
- cd /src/ && nimble install -y && \
- nimble install -y docopt && \
- nimble install -y c2nim@#3ec45c24585ebaed && \
- nim c -o:/usr/local/bin/nsb /src/docker/nsb.nim && \
- rm -rf /src/
=====================================
README.md
=====================================
@@ -17,7 +17,7 @@ too different to python.
If you use this library, please cite [the paper](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty358/4990493)
-Projects using `hts-nim` are accumulating [in the wiki](https://github.com/brentp/hts-nim/wiki/Examples)
+Projects using `hts-nim` are accumulating [in the wiki](https://github.com/brentp/hts-nim/wiki/Example-uses-of-hts-nim)
## Installation
@@ -29,7 +29,7 @@ Examples of `hts-nim` tools are available in the [hts-nim-tools repo](https://gi
below are examples of the syntax in this library see the [docs](https://brentp.github.io/hts-nim/) for more info:
-Also see examples and other repos using hts-nim in the [wiki](https://github.com/brentp/hts-nim/wiki/Examples)
+Also see examples and other repos using hts-nim in the [wiki](https://github.com/brentp/hts-nim/wiki/Example-uses-of-hts-nim)
## BAM / CRAM / SAM
=====================================
src/hts/private/hts_concat.nim
=====================================
@@ -8,9 +8,10 @@ elif defined(macosx):
else:
const
libname* = "libhts.so"
-when NimMajor < 1:
- type
- csize_t* = csize
+
+when (NimMajor, NimMinor) < (1, 1):
+ type
+ csize_t* = csize
##
## enum hts_fmt_option {
## // CRAM specific
=====================================
src/hts/vcf.nim
=====================================
@@ -73,6 +73,17 @@ var empty_samples: seq[string]
converter toInt(b:BCF_HEADER_TYPE): int = b.int
converter toCint(b:BCF_HEADER_TYPE): cint = b.cint
+proc destroy_variant(v:Variant) =
+ if v != nil and v.c != nil and v.own:
+ bcf_destroy(v.c)
+ v.c = nil
+ if v.p != nil:
+ free(v.p)
+
+proc destroy_format(f:Format) =
+ if f != nil and f.p != nil:
+ free(f.p)
+
proc n_samples*(v:VCF): int {.inline.} =
bcf_hdr_nsamples(v.header.hdr).int
@@ -175,15 +186,68 @@ proc remove_format*(h:Header, ID:string): Status =
bcf_hdr_remove(h.hdr, BCF_HEADER_TYPE.BCF_HL_FMT.cint, ID.cstring)
return Status(bcf_hdr_sync(h.hdr))
-proc info*(v:Variant): INFO {.inline, noInit.} =
- discard bcf_unpack(v.c, BCF_UN_STR or BCF_UN_FLT or BCF_UN_INFO)
- result = INFO(i:0, v:v)
+proc destroy_vcf(v:VCF) =
+ bcf_hdr_destroy(v.header.hdr)
+ if v.tidx != nil:
+ tbx_destroy(v.tidx)
+ if v.bidx != nil:
+ hts_idx_destroy(v.bidx)
+ if v.c != nil:
+ bcf_destroy(v.c)
+ if v.fname != "-" and v.fname != "/dev/stdin":
+ if v.hts != nil:
+ discard hts_close(v.hts)
+ v.hts = nil
+ else:
+ flushFile(stdout)
+
+var
+ errno* {.importc, header: "<errno.h>".}: cint
+
+proc strerror(errnum:cint): cstring {.importc, header: "<errno.h>", cdecl.}
+
+
+proc open*(v:var VCF, fname:string, mode:string="r", samples:seq[string]=empty_samples, threads:int=0): bool =
+ ## open a VCF at the given path
+ new(v, destroy_vcf)
+ var vmode = mode
+ if vmode[0] == 'w' and vmode.len == 1:
+ if fname.endswith(".gz"): vmode &= "z"
+ elif fname.endswith(".bcf"): vmode &= "b"
+
+ v.hts = hts_open(fname.cstring, vmode.cstring)
+ v.fname = fname
+ if v.hts == nil:
+ stderr.write_line "hts-nim/vcf: error opening file:" & fname & ". " & $strerror(errno)
+ return false
+
+ if mode[0] == 'w': return true
+
+ if mode[0] == 'r' and 0 != threads and 0 != hts_set_threads(v.hts, cint(threads)):
+ raise newException(ValueError, "error setting number of threads")
-proc destroy_format(f:Format) =
- if f != nil and f.p != nil:
- free(f.p)
-proc format*(v:Variant): FORMAT {.inline, noInit.} =
+ v.header = Header(hdr:bcf_hdr_read(v.hts))
+ if v.header.hdr == nil:
+ raise newException(OSError, &"[hts-nim/vcf] error reading VCF header from '{fname}'")
+ if samples.len != 0:
+ v.set_samples(samples)
+
+ v.c = bcf_init()
+
+ if v.c == nil:
+ stderr.write_line "hts-nim/vcf: error opening file:" & fname
+ return false
+
+ return true
+
+proc newVariant*(): Variant {.noInit.} =
+ ## make an empty variant.
+ new(result, destroy_variant)
+ result.c = bcf_init()
+ result.own = true
+
+proc format*(v:Variant): FORMAT {.inline.} =
discard bcf_unpack(v.c, BCF_UN_ALL)
new(result, destroy_format)
result.v = v
@@ -396,44 +460,6 @@ proc set*(i:INFO, key:string, values:var seq[int32]): Status {.inline.} =
values[0].addr.pointer, len(values).cint, BCF_HT_INT.cint)
return Status(ret.int)
-proc destroy_variant(v:Variant) =
- if v != nil and v.c != nil and v.own:
- bcf_destroy(v.c)
- v.c = nil
- if v.p != nil:
- free(v.p)
-
-proc from_string*(v: var Variant, h: Header, s:var string) =
- var str = kstring_t(s:s.cstring, l:s.len.csize_t, m:s.len.csize_t)
- if v == nil:
- new(v, destroy_variant)
- v.own = true
- if v.c == nil:
- v.c = bcf_init()
- if vcf_parse(str.addr, h.hdr, v.c) != 0:
- raise newException(ValueError, "hts-nim/Variant/from_string: error parsing variant:" & s)
-
-proc newVariant*(): Variant {.noInit.} =
- ## make an empty variant.
- new(result, destroy_variant)
- result.c = bcf_init()
- result.own = true
-
-proc destroy_vcf(v:VCF) =
- bcf_hdr_destroy(v.header.hdr)
- if v.tidx != nil:
- tbx_destroy(v.tidx)
- if v.bidx != nil:
- hts_idx_destroy(v.bidx)
- if v.c != nil:
- bcf_destroy(v.c)
- if v.fname != "-" and v.fname != "/dev/stdin":
- if v.hts != nil:
- discard hts_close(v.hts)
- v.hts = nil
- else:
- flushFile(stdout)
-
proc close*(v:VCF) =
if v.fname != "-" and v.fname != "/dev/stdin" and v.hts != nil:
if hts_close(v.hts) != 0:
@@ -469,44 +495,9 @@ proc write_variant*(v:VCF, variant:Variant): bool =
doAssert bcf_hdr_sync(variant.vcf.header.hdr) == 0
return bcf_write(v.hts, v.header.hdr, variant.c) == 0
-var
- errno* {.importc, header: "<errno.h>".}: cint
-
-proc strerror(errnum:cint): cstring {.importc, header: "<errno.h>", cdecl.}
-
-proc open*(v:var VCF, fname:string, mode:string="r", samples:seq[string]=empty_samples, threads:int=0): bool =
- ## open a VCF at the given path
- new(v, destroy_vcf)
- var vmode = mode
- if vmode[0] == 'w' and vmode.len == 1:
- if fname.endswith(".gz"): vmode &= "z"
- elif fname.endswith(".bcf"): vmode &= "b"
-
- v.hts = hts_open(fname.cstring, vmode.cstring)
- v.fname = fname
- if v.hts == nil:
- stderr.write_line "hts-nim/vcf: error opening file:" & fname & ". " & $strerror(errno)
- return false
-
- if mode[0] == 'w': return true
-
- if mode[0] == 'r' and 0 != threads and 0 != hts_set_threads(v.hts, cint(threads)):
- raise newException(ValueError, "error setting number of threads")
-
-
- v.header = Header(hdr:bcf_hdr_read(v.hts))
- if v.header.hdr == nil:
- raise newException(OSError, &"[hts-nim/vcf] error reading VCF header from '{fname}'")
- if samples.len != 0:
- v.set_samples(samples)
-
- v.c = bcf_init()
-
- if v.c == nil:
- stderr.write_line "hts-nim/vcf: error opening file:" & fname
- return false
-
- return true
+proc info*(v:Variant): INFO {.inline, noInit.} =
+ discard bcf_unpack(v.c, BCF_UN_STR or BCF_UN_FLT or BCF_UN_INFO)
+ result = INFO(i:0, v:v)
proc bcf_hdr_int2id(hdr: ptr bcf_hdr_t, typ: int, rid:int): cstring {.inline.} =
var v = cast[CPtr[bcf_idpair_t]](hdr.id[typ])
View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389
--
View it on GitLab: https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389
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