oceangenomics / mudskipper Goto Github PK
View Code? Open in Web Editor NEWA tool for projecting genomic alignments to transcriptomic coordinates
License: BSD 3-Clause "New" or "Revised" License
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mudskipper's Issues
Reading from SAM with multiple threads
In the implementation for getting all alignments of a query at once, I use bam::Reader::read() function. For some reason, when we turn on multi-threading for this reader, when reading from SAM, it gets stuck after reading all the records. However, that works fine for BAM!
Tried to re-produce the bug using a smaller code but failed. Needs more investigation!
Supporting supplementary alignments
Currently the code does not support supplementary alignments. An example from ERR188079 sample...
Here are the alignments from STAR:
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 chr2 190930498 255 35S40M = 190930482 0 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 chr2 190930482 255 74M1S = 190930514 67 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 83 chr2 190930514 255 35M40S = 190930482 -67 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:0 SA:Z:chr2,190930498,-,35S40M,255,0;
The first and third alignments in are supplementary. But mudskipper reports this:
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000412247.1 34 255 74M1S = 50 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000412247.1 50 255 35S40M = 34 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000409626.5 525 255 74M1S = 541 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000409626.5 541 255 35S40M = 525 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000457316.5 513 255 74M1S = 529 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000457316.5 529 255 35S40M = 513 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000320717.8 1735 255 74M1S = 1751 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000320717.8 1751 255 35S40M = 1735 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000409215.5 84 255 74M1S = 100 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000409215.5 100 255 35S40M = 84 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000409428.5 105 255 74M1S = 121 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000409428.5 121 255 35S40M = 105 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 163 ENST00000338435.8 1722 255 74M1S = 1738 -59 GTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATG BC@FFFFFHHGHGHIGIJJJCHHIGJJHIJIJGFHEIJIJIGGIGGEGIIIGIIIJJHIJIJCGGGIIJJJ;DHH NH:i:1 HI:i:1 AS:i:103 nM:i:2 NM:i:2
HWI-ST758:71:C06LWACXX:1:1101:2171:2414 2129 ENST00000338435.8 1738 255 35S40M = 1722 59 GTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGG FFDEHEAJJIJJJHGGIIJJJJJJJHHHHCEIGIHIJIGGIIJJIIIIJJJIGIGJHGIIIJHHHHFFFFFFC@@ NH:i:1 HI:i:1 AS:i:39 nM:i:0 NM:i:0 SA:Z:chr2,190930514,-,35M40S,255,0;
This makes things confusing for Salmon as it complains:
WARNING: Detected suspicious pair ---
The proper-pair statuses are inconsistent:
read1 [HWI-ST758:71:C06LWACXX:1:1101:2171:2414] : proper-pair; mapped; matemapped
read2 : [HWI-ST758:71:C06LWACXX:1:1101:2171:2414] : no proper-pair; mapped; matemapped
test_bam2bam fails
The test test_bam2bam on line 32 of tests/bam_test.rs currently fails. It was failing before because the return type of read_and_process was not right. I fixed that, but this test is still failing. It should fail to find / write 33 records, but has 0. Actually since bam2bam didn't return an integer, it is unclear how this value is to be calculated, so I took a best guess (probably wrong). Can you advise @sjbaker47 and @HosseinAsghari (cc @mohsenzakeri, @haghshenas).
Thanks!
Rob
Inconsistent CIGAR strings
On sample ERR188079, Salmon prints this warning message when consuming mudskipper output generated from STAR alignments:
[2021-11-17 20:55:50.696] [jointLog] [warning] (in logLikelihood()) CIGAR string for read [HWI-ST758:71:C06LWACXX:1:1101:2482:20383] seems inconsistent. It refers to non-existant positions in the reference! Transcript name is ENST00000528619.5, length is 731, id is 145760. Read things refid is 145766
[2021-11-17 20:55:50.696] [jointLog] [warning] (in logLikelihood()) CIGAR string for read [HWI-ST758:71:C06LWACXX:1:1101:2482:20383] seems inconsistent. It refers to non-existant positions in the reference! Transcript name is ENST00000529421.5, length is 801, id is 145761. Read things refid is 145757
[2021-11-17 20:55:50.696] [jointLog] [warning] (in logLikelihood()) CIGAR string for read [HWI-ST758:71:C06LWACXX:1:1101:2482:20383] seems inconsistent. It refers to non-existant positions in the reference! Transcript name is ENST00000379060.8, length is 764, id is 145766. Read things refid is 145759
transcript index = 569, transcript length = 348
Handle unmapped reads more properly
Currently if one mate of the read is aligned while the other mate is unaligned, mudskipper treats it as a single-end read. This is not quite right. In the transcriptome bam, also one end should remain unmapped (with proper bit in FLAG set and also * as target).
BAM record is not updated properly for reverse orientation transcripts
If an alignment is being projected to a transcript that is on the reverse strand, then CIGAR, sequence and quality should be reversed (or reverse complemented).
Compile errors
MacBook M1 Max Pro
Dockerfile:
FROM ubuntu:focal as build
ARG MUDSKIPPER_VERSION
ENV DEBIAN_FRONTEND=noninteractive
ENV PATH=/root/.cargo/bin:$PATH
ADD https://github.com/OceanGenomics/mudskipper/archive/refs/tags/v${MUDSKIPPER_VERSION}.tar.gz mudskipper.tgz
RUN apt update \
&& apt install -y curl build-essential cmake \
&& curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y \
&& mkdir mudskipper \
&& tar -C mudskipper --strip-components=1 -xzf mudskipper.tgz \
&& cd mudskipper \
&& cargo build --release \
&& mv target/release/mudskipper /usr/local/bin
FROM ubuntu:focal
COPY --from=build /usr/local/bin/mudskipper /usr/local/bin/mudskipper
Docker command: docker build -f Dockerfile.mudskipper -t mudskipper --build-arg MUDSKIPPER_VERSION=0.1.0 .
Errors:
#0 131.0 error[E0308]: mismatched types
#0 131.0 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:152:16
#0 131.0 |
#0 131.0 152 | s: sam_copy.as_ptr() as *mut i8,
#0 131.0 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.0 |
#0 131.0 = note: expected raw pointer `*mut u8`
#0 131.0 found raw pointer `*mut i8`
#0 131.0
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:583:17
#0 131.1 |
#0 131.1 583 | c_str.as_ptr() as *mut i8,
#0 131.1 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:678:49
#0 131.1 |
#0 131.1 678 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::<i8>());
#0 131.1 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*const i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:798:21
#0 131.1 |
#0 131.1 798 | ctag,
#0 131.1 | ^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:799:21
#0 131.1 |
#0 131.1 799 | b'A' as i8,
#0 131.1 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1 |
#0 131.1 799 | (b'A' as i8).try_into().unwrap(),
#0 131.1 | + +++++++++++++++++++++
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:805:21
#0 131.1 |
#0 131.1 805 | ctag,
#0 131.1 | ^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:806:21
#0 131.1 |
#0 131.1 806 | b'c' as i8,
#0 131.1 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1 |
#0 131.1 806 | (b'c' as i8).try_into().unwrap(),
#0 131.1 | + +++++++++++++++++++++
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:812:21
#0 131.1 |
#0 131.1 812 | ctag,
#0 131.1 | ^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:813:21
#0 131.1 |
#0 131.1 813 | b'C' as i8,
#0 131.1 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1 |
#0 131.1 813 | (b'C' as i8).try_into().unwrap(),
#0 131.1 | + +++++++++++++++++++++
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:819:21
#0 131.1 |
#0 131.1 819 | ctag,
#0 131.1 | ^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:820:21
#0 131.1 |
#0 131.1 820 | b's' as i8,
#0 131.1 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1 |
#0 131.1 820 | (b's' as i8).try_into().unwrap(),
#0 131.1 | + +++++++++++++++++++++
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:826:21
#0 131.1 |
#0 131.1 826 | ctag,
#0 131.1 | ^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:827:21
#0 131.1 |
#0 131.1 827 | b'S' as i8,
#0 131.1 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1 |
#0 131.1 827 | (b'S' as i8).try_into().unwrap(),
#0 131.1 | + +++++++++++++++++++++
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:833:21
#0 131.1 |
#0 131.1 833 | ctag,
#0 131.1 | ^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 = note: expected raw pointer `*const u8`
#0 131.1 found raw pointer `*mut i8`
#0 131.1
#0 131.1 error[E0308]: mismatched types
#0 131.1 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:834:21
#0 131.1 |
#0 131.1 834 | b'i' as i8,
#0 131.1 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.1 |
#0 131.1 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.1 |
#0 131.1 834 | (b'i' as i8).try_into().unwrap(),
#0 131.1 | + +++++++++++++++++++++
#0 131.1
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:840:21
#0 131.2 |
#0 131.2 840 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:841:21
#0 131.2 |
#0 131.2 841 | b'I' as i8,
#0 131.2 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2 |
#0 131.2 841 | (b'I' as i8).try_into().unwrap(),
#0 131.2 | + +++++++++++++++++++++
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:847:21
#0 131.2 |
#0 131.2 847 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:848:21
#0 131.2 |
#0 131.2 848 | b'f' as i8,
#0 131.2 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2 |
#0 131.2 848 | (b'f' as i8).try_into().unwrap(),
#0 131.2 | + +++++++++++++++++++++
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:855:21
#0 131.2 |
#0 131.2 855 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:856:21
#0 131.2 |
#0 131.2 856 | b'd' as i8,
#0 131.2 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2 |
#0 131.2 856 | (b'd' as i8).try_into().unwrap(),
#0 131.2 | + +++++++++++++++++++++
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:864:25
#0 131.2 |
#0 131.2 864 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:865:25
#0 131.2 |
#0 131.2 865 | b'Z' as i8,
#0 131.2 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2 |
#0 131.2 865 | (b'Z' as i8).try_into().unwrap(),
#0 131.2 | + +++++++++++++++++++++
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:874:25
#0 131.2 |
#0 131.2 874 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:875:25
#0 131.2 |
#0 131.2 875 | b'H' as i8,
#0 131.2 | ^^^^^^^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 help: you can convert an `i8` to a `u8` and panic if the converted value doesn't fit
#0 131.2 |
#0 131.2 875 | (b'H' as i8).try_into().unwrap(),
#0 131.2 | + +++++++++++++++++++++
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:884:25
#0 131.2 |
#0 131.2 884 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:891:25
#0 131.2 |
#0 131.2 891 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.2 error[E0308]: mismatched types
#0 131.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:900:25
#0 131.2 |
#0 131.2 900 | ctag,
#0 131.2 | ^^^^ expected `u8`, found `i8`
#0 131.2 |
#0 131.2 = note: expected raw pointer `*const u8`
#0 131.2 found raw pointer `*mut i8`
#0 131.2
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:907:25
#0 131.3 |
#0 131.3 907 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:916:25
#0 131.3 |
#0 131.3 916 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:923:25
#0 131.3 |
#0 131.3 923 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:932:25
#0 131.3 |
#0 131.3 932 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:939:25
#0 131.3 |
#0 131.3 939 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:948:25
#0 131.3 |
#0 131.3 948 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.3 error[E0308]: mismatched types
#0 131.3 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:955:25
#0 131.3 |
#0 131.3 955 | ctag,
#0 131.3 | ^^^^ expected `u8`, found `i8`
#0 131.3 |
#0 131.3 = note: expected raw pointer `*const u8`
#0 131.3 found raw pointer `*mut i8`
#0 131.3
#0 131.4 error[E0308]: mismatched types
#0 131.4 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:964:25
#0 131.4 |
#0 131.4 964 | ctag,
#0 131.4 | ^^^^ expected `u8`, found `i8`
#0 131.4 |
#0 131.4 = note: expected raw pointer `*const u8`
#0 131.4 found raw pointer `*mut i8`
#0 131.4
#0 131.4 error[E0308]: mismatched types
#0 131.4 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:971:25
#0 131.4 |
#0 131.4 971 | ctag,
#0 131.4 | ^^^^ expected `u8`, found `i8`
#0 131.4 |
#0 131.4 = note: expected raw pointer `*const u8`
#0 131.4 found raw pointer `*mut i8`
#0 131.4
#0 131.4 error[E0308]: mismatched types
#0 131.4 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:980:25
#0 131.4 |
#0 131.4 980 | ctag,
#0 131.4 | ^^^^ expected `u8`, found `i8`
#0 131.4 |
#0 131.4 = note: expected raw pointer `*const u8`
#0 131.4 found raw pointer `*mut i8`
#0 131.4
#0 131.4 error[E0308]: mismatched types
#0 131.4 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:987:25
#0 131.4 |
#0 131.4 987 | ctag,
#0 131.4 | ^^^^ expected `u8`, found `i8`
#0 131.4 |
#0 131.4 = note: expected raw pointer `*const u8`
#0 131.4 found raw pointer `*mut i8`
#0 131.4
#0 131.4 error[E0308]: mismatched types
#0 131.4 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:1009:17
#0 131.4 |
#0 131.4 1009 | c_str.as_ptr() as *mut i8,
#0 131.4 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.4 |
#0 131.4 = note: expected raw pointer `*const u8`
#0 131.4 found raw pointer `*mut i8`
#0 131.4
#0 131.5 error[E0308]: mismatched types
#0 131.5 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:268:55
#0 131.5 |
#0 131.5 268 | let _ = htslib::sam_hdr_line_name(header, b"SQ".as_ptr().cast::<i8>(), 0);
#0 131.5 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5 |
#0 131.5 = note: expected raw pointer `*const u8`
#0 131.5 found raw pointer `*const i8`
#0 131.5
#0 131.5 Compiling bio v0.41.0
#0 131.5 error[E0308]: mismatched types
#0 131.5 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:943:17
#0 131.5 |
#0 131.5 943 | text as *const i8,
#0 131.5 | ^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5 |
#0 131.5 = note: expected raw pointer `*const u8`
#0 131.5 found raw pointer `*const i8`
#0 131.5
#0 131.5 error[E0308]: mismatched types
#0 131.5 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:946:27
#0 131.5 |
#0 131.5 946 | (*rec).text = text as *mut i8;
#0 131.5 | ----------- ^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5 | |
#0 131.5 | expected due to the type of this binding
#0 131.5 |
#0 131.5 = note: expected raw pointer `*mut u8`
#0 131.5 found raw pointer `*mut i8`
#0 131.5
#0 131.5 error[E0308]: mismatched types
#0 131.5 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:1212:66
#0 131.5 |
#0 131.5 1212 | let rec = htslib::sam_hdr_parse((l_text + 1) as u64, text as *const i8);
#0 131.5 | ^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.5 |
#0 131.5 = note: expected raw pointer `*const u8`
#0 131.5 found raw pointer `*const i8`
#0 131.5
#0 131.6 error[E0308]: mismatched types
#0 131.6 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/mod.rs:1213:27
#0 131.6 |
#0 131.6 1213 | (*rec).text = text as *mut i8;
#0 131.6 | ----------- ^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6 | |
#0 131.6 | expected due to the type of this binding
#0 131.6 |
#0 131.6 = note: expected raw pointer `*mut u8`
#0 131.6 found raw pointer `*mut i8`
#0 131.6
#0 131.6 error[E0308]: mismatched types
#0 131.6 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:118:17
#0 131.6 |
#0 131.6 118 | name_pointers.as_ptr() as *const *mut i8,
#0 131.6 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6 |
#0 131.6 = note: expected raw pointer `*const *mut u8`
#0 131.6 found raw pointer `*const *mut i8`
#0 131.6
#0 131.6 error[E0308]: mismatched types
#0 131.6 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:341:17
#0 131.6 |
#0 131.6 341 | c_str.as_ptr() as *mut i8,
#0 131.6 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6 |
#0 131.6 = note: expected raw pointer `*const u8`
#0 131.6 found raw pointer `*mut i8`
#0 131.6
#0 131.6 error[E0308]: mismatched types
#0 131.6 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:366:17
#0 131.6 |
#0 131.6 366 | c_str_tag.as_ptr() as *mut i8,
#0 131.6 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6 |
#0 131.6 = note: expected raw pointer `*const u8`
#0 131.6 found raw pointer `*mut i8`
#0 131.6
#0 131.6 error[E0308]: mismatched types
#0 131.6 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:403:17
#0 131.6 |
#0 131.6 403 | c_str.as_ptr() as *const i8,
#0 131.6 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.6 |
#0 131.6 = note: expected raw pointer `*const u8`
#0 131.6 found raw pointer `*const i8`
#0 131.6
#0 131.7 error[E0308]: mismatched types
#0 131.7 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/header.rs:431:17
#0 131.7 |
#0 131.7 431 | c_str.as_ptr() as *const i8,
#0 131.7 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7 |
#0 131.7 = note: expected raw pointer `*const u8`
#0 131.7 found raw pointer `*const i8`
#0 131.7
#0 131.7 error[E0308]: mismatched types
#0 131.7 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:319:68
#0 131.7 |
#0 131.7 319 | htslib::bcf_update_id(self.header().inner, self.inner, c_str.as_ptr() as *mut i8)
#0 131.7 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7 |
#0 131.7 = note: expected raw pointer `*const u8`
#0 131.7 found raw pointer `*mut i8`
#0 131.7
#0 131.7 error[E0308]: mismatched types
#0 131.7 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:332:68
#0 131.7 |
#0 131.7 332 | htslib::bcf_update_id(self.header().inner, self.inner, c_str.as_ptr() as *mut i8)
#0 131.7 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7 |
#0 131.7 = note: expected raw pointer `*const u8`
#0 131.7 found raw pointer `*mut i8`
#0 131.7
#0 131.7 error[E0308]: mismatched types
#0 131.7 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:344:73
#0 131.7 |
#0 131.7 344 | if unsafe { htslib::bcf_add_id(self.header().inner, self.inner, c_str.as_ptr() as *mut i8) }
#0 131.7 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7 |
#0 131.7 = note: expected raw pointer `*const u8`
#0 131.7 found raw pointer `*mut i8`
#0 131.7
#0 131.7 error[E0308]: mismatched types
#0 131.7 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:591:17
#0 131.7 |
#0 131.7 591 | ptrs.as_mut_ptr(),
#0 131.7 | ^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.7 |
#0 131.7 = note: expected raw pointer `*mut *const u8`
#0 131.7 found raw pointer `*mut *const i8`
#0 131.7
#0 131.8 error[E0308]: mismatched types
#0 131.8 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:825:17
#0 131.8 |
#0 131.8 825 | tag_c_str.as_ptr() as *mut i8,
#0 131.8 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.8 |
#0 131.8 = note: expected raw pointer `*const u8`
#0 131.8 found raw pointer `*mut i8`
#0 131.8
#0 131.8 error[E0308]: mismatched types
#0 131.8 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:872:17
#0 131.8 |
#0 131.8 872 | tag_c_str.as_ptr() as *mut i8,
#0 131.8 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.8 |
#0 131.8 = note: expected raw pointer `*const u8`
#0 131.8 found raw pointer `*mut i8`
#0 131.8
#0 131.8 error[E0308]: mismatched types
#0 131.8 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:873:17
#0 131.8 |
#0 131.8 873 | c_ptrs.as_slice().as_ptr() as *mut *const i8,
#0 131.8 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.8 |
#0 131.8 = note: expected raw pointer `*mut *const u8`
#0 131.8 found raw pointer `*mut *const i8`
#0 131.8
#0 131.9 error[E0308]: mismatched types
#0 131.9 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:918:17
#0 131.9 |
#0 131.9 918 | tag_c_str.as_ptr() as *mut i8,
#0 131.9 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9 |
#0 131.9 = note: expected raw pointer `*const u8`
#0 131.9 found raw pointer `*mut i8`
#0 131.9
#0 131.9 error[E0308]: mismatched types
#0 131.9 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:973:17
#0 131.9 |
#0 131.9 973 | tag_c_str.as_ptr() as *mut i8,
#0 131.9 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9 |
#0 131.9 = note: expected raw pointer `*const u8`
#0 131.9 found raw pointer `*mut i8`
#0 131.9
#0 131.9 error[E0308]: mismatched types
#0 131.9 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:1234:17
#0 131.9 |
#0 131.9 1234 | c_str.as_ptr() as *mut i8,
#0 131.9 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9 |
#0 131.9 = note: expected raw pointer `*const u8`
#0 131.9 found raw pointer `*mut i8`
#0 131.9
#0 131.9 error[E0308]: mismatched types
#0 131.9 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:1349:17
#0 131.9 |
#0 131.9 1349 | c_str.as_ptr() as *mut i8,
#0 131.9 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 131.9 |
#0 131.9 = note: expected raw pointer `*const u8`
#0 131.9 found raw pointer `*mut i8`
#0 131.9
#0 132.0 error[E0308]: mismatched types
#0 132.0 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bcf/record.rs:1385:17
#0 132.0 |
#0 132.0 1385 | c_str.as_ptr() as *mut i8,
#0 132.0 | ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
#0 132.0 |
#0 132.0 = note: expected raw pointer `*const u8`
#0 132.0 found raw pointer `*mut i8`
#0 132.0
#0 132.1 For more information about this error, try `rustc --explain E0308`.
#0 132.1 error: could not compile `rust-htslib` due to 62 previous errors
#0 132.1 warning: build failed, waiting for other jobs to finish...
#0 137.5 error: build failed
Support overhanging alignments
Currently if a read is overhanging on one end of the transcript, it will not be reported. However, we should improve on this by softclipping the overhanging bases.
Off by one error in setting the number of threads
In setting the number of threads for BAM/SAM reader/writer, the function accepts the extra number of threads, not the total. That means the current implementation is assigning one more threads in case of multi-threading.
Compiling error on MacOS
Hi team,
The following error on MacOS:
The following warnings were emitted during compilation:
warning: curl/lib/connect.c: In function 'singleipconnect':
warning: curl/lib/connect.c:1279:10: warning: implicit declaration of function '__builtin_available'; did you mean '__builtin_scalbl'? [-Wimplicit-function-declaration]
warning: 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, *)) {
warning: | ^~~~~~~~~~~~~~~~~~~
warning: | __builtin_scalbl
warning: curl/lib/connect.c:1279:30: error: 'macOS' undeclared (first use in this function)
warning: 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, *)) {
warning: | ^~~~~
warning: curl/lib/connect.c:1279:30: note: each undeclared identifier is reported only once for each function it appears in
warning: curl/lib/connect.c:1279:35: error: expected ')' before numeric constant
warning: 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, *)) {
warning: | ~ ^~~~~~
warning: | )
error: failed to run custom build command for curl-sys v0.4.52+curl-7.81.0
Caused by:
process didn't exit successfully: /Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-9b4192310196e29f/build-script-build (exit status: 1)
--- stdout
cargo:rerun-if-changed=curl
cargo:rustc-link-lib=clang_rt.osx
cargo:rustc-link-search=/opt/homebrew/Cellar/llvm/13.0.1/lib/clang/13.0.1/lib/darwin
cargo:root=/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out
cargo:include=/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/include
cargo:static=1
cargo:rustc-cfg=libcurl_vendored
cargo:rustc-cfg=link_libz
/Library/Developer/CommandLineTools
unable to determine Xcode version, assuming >= 9
TARGET = Some("aarch64-apple-darwin")
OPT_LEVEL = Some("3")
HOST = Some("aarch64-apple-darwin")
CC_aarch64-apple-darwin = None
CC_aarch64_apple_darwin = None
HOST_CC = None
CC = None
CFLAGS_aarch64-apple-darwin = None
CFLAGS_aarch64_apple_darwin = None
HOST_CFLAGS = None
CFLAGS = None
CRATE_CC_NO_DEFAULTS = None
DEBUG = Some("false")
CARGO_CFG_TARGET_FEATURE = Some("aes,crc,dit,dotprod,dpb,dpb2,fcma,fhm,flagm,fp,fp16,frintts,jsconv,lor,lse,neon,pan,pauth,pmuv3,ras,rcpc,rcpc2,rdm,sb,sha2,sha3,ssbs,v8.1a,v8.2a,v8.3a,v8.4a,vh")
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/conncache.o" "-c" "curl/lib/conncache.c"
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/asyn-thread.o" "-c" "curl/lib/asyn-thread.c"
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/content_encoding.o" "-c" "curl/lib/content_encoding.c"
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/bufref.o" "-c" "curl/lib/bufref.c"
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/altsvc.o" "-c" "curl/lib/altsvc.c"
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/base64.o" "-c" "curl/lib/base64.c"
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/connect.o" "-c" "curl/lib/connect.c"
cargo:warning=curl/lib/connect.c: In function 'singleipconnect':
cargo:warning=curl/lib/connect.c:1279:10: warning: implicit declaration of function '__builtin_available'; did you mean '__builtin_scalbl'? [-Wimplicit-function-declaration]
cargo:warning= 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, *)) {
cargo:warning= | ^~~~~~~~~~~~~~~~~~~
cargo:warning= | __builtin_scalbl
cargo:warning=curl/lib/connect.c:1279:30: error: 'macOS' undeclared (first use in this function)
cargo:warning= 1279 | if(builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) {
cargo:warning= | ^~~~~
cargo:warning=curl/lib/connect.c:1279:30: note: each undeclared identifier is reported only once for each function it appears in
cargo:warning=curl/lib/connect.c:1279:35: error: expected ')' before numeric constant
cargo:warning= 1279 | if(__builtin_available(macOS 10.11, iOS 9.0, tvOS 9.0, watchOS 2.0, )) {
cargo:warning= | ~ ^~~~~~
cargo:warning= | )
exit status: 1
running: "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/cookie.o" "-c" "curl/lib/cookie.c"
exit status: 0
exit status: 0
exit status: 0
exit status: 0
exit status: 0
exit status: 0
exit status: 0
--- stderr
fatal: not a git repository (or any of the parent directories): .git
error occurred: Command "cc" "-O3" "-ffunction-sections" "-fdata-sections" "-fPIC" "-arch" "arm64" "-I" "curl/lib" "-I" "curl/include" "-I" "/Users/jianshuzhao/Github/mudskipper/target/release/build/libz-sys-4a0742c61ab93e89/out/include" "-fvisibility=hidden" "-DBUILDING_LIBCURL" "-DCURL_DISABLE_DICT" "-DCURL_DISABLE_GOPHER" "-DCURL_DISABLE_IMAP" "-DCURL_DISABLE_LDAP" "-DCURL_DISABLE_LDAPS" "-DCURL_DISABLE_POP3" "-DCURL_DISABLE_RTSP" "-DCURL_DISABLE_SMB" "-DCURL_DISABLE_SMTP" "-DCURL_DISABLE_TELNET" "-DCURL_DISABLE_TFTP" "-DCURL_STATICLIB" "-DENABLE_IPV6" "-DHAVE_ASSERT_H" "-DOS="unknown"" "-DHAVE_ZLIB_H" "-DHAVE_LONGLONG" "-DHAVE_LIBZ" "-DHAVE_BOOL_T" "-DHAVE_STDBOOL_H" "-DHAVE_GETADDRINFO" "-DHAVE_GETPEERNAME" "-DHAVE_GETSOCKNAME" "-DCURL_DISABLE_NTLM" "-DUSE_SECTRANSP" "-DHAVE_BUILTIN_AVAILABLE=1" "-DRECV_TYPE_ARG1=int" "-DHAVE_PTHREAD_H" "-DHAVE_ARPA_INET_H" "-DHAVE_ERRNO_H" "-DHAVE_FCNTL_H" "-DHAVE_NETDB_H" "-DHAVE_NETINET_IN_H" "-DHAVE_NETINET_TCP_H" "-DHAVE_POLL_H" "-DHAVE_FCNTL_O_NONBLOCK" "-DHAVE_SYS_SELECT_H" "-DHAVE_SYS_STAT_H" "-DHAVE_UNISTD_H" "-DHAVE_RECV" "-DHAVE_SELECT" "-DHAVE_SEND" "-DHAVE_SOCKET" "-DHAVE_STERRROR_R" "-DHAVE_SOCKETPAIR" "-DHAVE_STRUCT_TIMEVAL" "-DHAVE_SYS_UN_H" "-DUSE_THREADS_POSIX" "-DUSE_UNIX_SOCKETS" "-DRECV_TYPE_ARG2=void*" "-DRECV_TYPE_ARG3=size_t" "-DRECV_TYPE_ARG4=int" "-DRECV_TYPE_RETV=ssize_t" "-DSEND_QUAL_ARG2=const" "-DSEND_TYPE_ARG1=int" "-DSEND_TYPE_ARG2=void*" "-DSEND_TYPE_ARG3=size_t" "-DSEND_TYPE_ARG4=int" "-DSEND_TYPE_RETV=ssize_t" "-DSIZEOF_CURL_OFF_T=8" "-DSIZEOF_INT=4" "-DSIZEOF_SHORT=2" "-D__APPLE__" "-Dmacintosh" "-DHAVE_MACH_ABSOLUTE_TIME" "-DSIZEOF_SSIZE_T=8" "-DSIZEOF_SIZE_T=8" "-DSIZEOF_LONG=8" "-o" "/Users/jianshuzhao/Github/mudskipper/target/release/build/curl-sys-fd2b0ac6e5689972/out/build/curl/lib/connect.o" "-c" "curl/lib/connect.c" with args "cc" did not execute successfully (status code exit status: 1).
warning: build failed, waiting for other jobs to finish...
error: build failed
Any idea
Thanks,
Jianshu
Wrong pairing of alignments
Again from ERR188079 sample... STAR reports:
HWI-ST758:71:C06LWACXX:1:1101:11011:4002 163 chr22 37225967 255 74M1S = 37226011 748 CGGGGTGCCATCAGGCTTTGGGTGGGGATCCTGGAGGATCAGACCCATCTAGGTGGGAGCGCTGGGGTGCAACCC @@CFFADDDFHHFIIIJIIJJJHJIGIJFIIIJJHIJGIJJJIIJJJJHHHHHHFFDBDCDDDDDDD8@BCDDDD NH:i:1 HI:i:1 AS:i:147 nM:i:0 NM:i:0
HWI-ST758:71:C06LWACXX:1:1101:11011:4002 83 chr22 37226011 255 29M631N44M2S = 37225967 -748 CCATCTAGGTGGGAGCGCTGGGGTGCAACCCCTAGAGGAGGCTGCAGGCGCGCTTCTGCTGCCGCGTGGGCTGGG DDDDDDDDDCDDDDDDDDDDDDDDBDB@DDEEECFEFFFHHHGIJIJJIIJFIJJJIJJJJJHHHHHFFFFFC@C NH:i:1 HI:i:1 AS:i:147 nM:i:0 NM:i:0
while mudskipper reports:
HWI-ST758:71:C06LWACXX:1:1101:11011:4002 99 ENST00000406508.5 662 255 73M2S = 705 -32 CCATCTAGGTGGGAGCGCTGGGGTGCAACCCCTAGAGGAGGCTGCAGGCGCGCTTCTGCTGCCGCGTGGGCTGGG DDDDDDDDDCDDDDDDDDDDDDDDBDB@DDEEECFEFFFHHHGIJIJJIIJFIJJJIJJJJJHHHHHFFFFFC@C NH:i:1 HI:i:1 AS:i:147 nM:i:0 NM:i:0
HWI-ST758:71:C06LWACXX:1:1101:11024:4004 147 ENST00000406508.5 705 255 74M1S = 662 32 CGGGGTGCCATCAGGCTTTGGGTGGGGATCCTGGAGGATCAGACCCATCTAGGTGGGAGCGCTGGGGTGCAACCC ?@@D==@BDFBC<?BBDG?DHHIG:@@G@?DDHJGGIDFGIGIEIIHHFHHHG=CBDACBDDDDDDD8@DDDCDD NH:i:1 HI:i:1 AS:i:149 nM:i:0 NM:i:0
HWI-ST758:71:C06LWACXX:1:1101:11011:4002 99 ENST00000249071.11 659 255 73M2S = 702 -32 CCATCTAGGTGGGAGCGCTGGGGTGCAACCCCTAGAGGAGGCTGCAGGCGCGCTTCTGCTGCCGCGTGGGCTGGG DDDDDDDDDCDDDDDDDDDDDDDDBDB@DDEEECFEFFFHHHGIJIJJIIJFIJJJIJJJJJHHHHHFFFFFC@C NH:i:1 HI:i:1 AS:i:147 nM:i:0 NM:i:0
HWI-ST758:71:C06LWACXX:1:1101:11024:4004 147 ENST00000249071.11 702 255 74M1S = 659 32 CGGGGTGCCATCAGGCTTTGGGTGGGGATCCTGGAGGATCAGACCCATCTAGGTGGGAGCGCTGGGGTGCAACCC ?@@D==@BDFBC<?BBDG?DHHIG:@@G@?DDHJGGIDFGIGIEIIHHFHHHG=CBDACBDDDDDDD8@DDDCDD NH:i:1 HI:i:1 AS:i:149 nM:i:0 NM:i:0
HWI-ST758:71:C06LWACXX:1:1101:11011:4002 99 ENST00000481215.1 363 255 73M2S = 406 -32 CCATCTAGGTGGGAGCGCTGGGGTGCAACCCCTAGAGGAGGCTGCAGGCGCGCTTCTGCTGCCGCGTGGGCTGGG DDDDDDDDDCDDDDDDDDDDDDDDBDB@DDEEECFEFFFHHHGIJIJJIIJFIJJJIJJJJJHHHHHFFFFFC@C NH:i:1 HI:i:1 AS:i:147 nM:i:0 NM:i:0
HWI-ST758:71:C06LWACXX:1:1101:11024:4004 147 ENST00000481215.1 406 255 74M1S = 363 32 CGGGGTGCCATCAGGCTTTGGGTGGGGATCCTGGAGGATCAGACCCATCTAGGTGGGAGCGCTGGGGTGCAACCC ?@@D==@BDFBC<?BBDG?DHHIG:@@G@?DDHJGGIDFGIGIEIIHHFHHHG=CBDACBDDDDDDD8@DDDCDD NH:i:1 HI:i:1 AS:i:149 nM:i:0 NM:i:0
Salmon correctly throws warning:
WARNING: Detected suspicious pair ---
The names are different:
read1 : HWI-ST758:71:C06LWACXX:1:1101:11011:4002
read2 : HWI-ST758:71:C06LWACXX:1:1101:11024:4004
Differences in quantification when using transcriptome BAM from Muskipper or STAR
Hi, I would like to report some differences in the quantification produced by Salmon when doing pseudoalignment, when using transcriptomic BAM produced by STAR and when using the transcriptomic BAM produced by Mudskipper.
Pearson correlation of log2(raw counts)
| salmon_mudskipper | salmon_star | salmon quant | |
|---|---|---|---|
| salmon_mudskipper | 1.000000 | 0.611192 | 0.578433 |
| salmon_star | 0.611192 | 1.000000 | 0.942535 |
| salmon quant | 0.578433 | 0.942535 | 1.000000 |
The results when using the transcriptomic BAM produced by STAR seems much more similar to the results when using the transcriptomic BAM from Mudskipper
Following is the command lines and software version.
STAR=v2.7.8a
mudskipper=commit 3717465
salmon=1.9.0
STAR --runThreadN 10 --genomeDir /ensembl/hs104/ --readFilesIn SRR3670977.fastq --outSAMtype BAM Unsorted --genomeLoad NoSharedMemory --limitOutSJcollapsed 5000000 --outSAMunmapped Within --quantMode TranscriptomeSAM GeneCounts
mudskipper bulk --gtf Homo_sapiens.GRCh38.104.primary_assembly.gtf --alignment Aligned.out.bam --out Aligned.mudskipperout.bam
salmon quant --libType A --alignments Aligned.mudskipperout.bam --targets Homo_sapiens.GRCh38.cdna.all.104.fa.gz --output salmon_mudskipper --threads 10
salmon quant --libType A --alignments Aligned.toTranscriptome.out.bam --targets Homo_sapiens.GRCh38.cdna.all.104.fa.gz --output salmon_star --threads 10
salmon quant --libType A --threads 10 --index Homo_sapiens.GRCh38.cdna.all.104.salmon_index --output salmon_quant -r SRR3670977.fastq
I wanted to know if you have some hints of what could happening here.
Negative coordinate in output BAM
I have seen a case where the output BAM record has negative coordinate! Sample input BAM file is attached. For this test case, Mudskipper should be run using the following GTF.
http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_35/gencode.v35.annotation.gtf.gz
cargo build --release!
cargo build --release running for Mudskipper installation get me the error, Your help to fix it is so appreciated!
error[E0308]: mismatched types
--> src/annotation.rs:198:25
|
198 | strand: exon_strand,
| ^^^^^^^^^^^ expected enum Strand, found enum bio_types::strand::Strand
|
= note: perhaps two different versions of crate bio_types are being used?
For more information about this error, try rustc --explain E0308.
error: could not compile mudskipper due to previous error
Build a unmapped barcode frequency table
For some advanced features of alevin-fry, it needs a map that contains the number of unmapped reads for each barcode. Since that map is not required for performing quantification using alevin-fry for now, mudskipper creates an empty map. This should be modified with the proper content.
Disagreement with the annotation when there is a spliced alignment
The code doesn't properly check the splicing when converting alignments.
For example in an alignment with CIGAR 9M477N41M86N25M, the middle matched segment should extend to the boundaries of the exon on both sides.
That means some spurious alignments might be reported due to this bug.
'main' panicked at 'index out of bounds: the len is 1 but the index is 1'
Built the index first using gencode v40
mudskipper index --gtf /SAN/vyplab/vyplab_reference_genomes/annotation/human/GRCh38/gencode.v40.annotation.gtf --dir-index /SAN/vyplab/vyplab_reference_genomes/mudskipper_indices/human.gencode.v40
And then tried to convert with
mudskipper bulk --index /SAN/vyplab/vyplab_reference_genomes/mudskipper_indices/human.gencode.v40/ --alignment my.sorted.bam --out my.mud.bam --threads 4
However this freaks out immediately with:
[2022-05-02T12:43:07Z INFO mudskipper] Mudskipper started...
[2022-05-02T12:43:07Z INFO mudskipper::annotation] Loading parsed GTF...
[2022-05-02T12:43:08Z INFO mudskipper::bam] Number of reference sequences: 246624
[2022-05-02T12:43:09Z INFO mudskipper::bam] thread count: 4 in total
[2022-05-02T12:43:09Z INFO mudskipper::bam] thread count: 2 for reading
[2022-05-02T12:43:09Z INFO mudskipper::bam] thread count: 2 for writing
thread 'main' panicked at 'index out of bounds: the len is 1 but the index is 1', src/query_bam_records.rs:165:33
stack backtrace:
0: 0x5599e7546c2d - std::backtrace_rs::backtrace::libunwind::trace::hee598835bc88d35b
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/../../backtrace/src/backtrace/libunwind.rs:93:5
1: 0x5599e7546c2d - std::backtrace_rs::backtrace::trace_unsynchronized::h9cdc730ba5cf5d72
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5
2: 0x5599e7546c2d - std::sys_common::backtrace::_print_fmt::h75aeaf7ed30e43fa
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/sys_common/backtrace.rs:66:5
3: 0x5599e7546c2d - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::h606862f787600875
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/sys_common/backtrace.rs:45:22
4: 0x5599e7569a9c - core::fmt::write::he803f0f418caf762
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/core/src/fmt/mod.rs:1190:17
5: 0x5599e7542fc8 - std::io::Write::write_fmt::h70bc45872f37e7bb
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/io/mod.rs:1657:15
6: 0x5599e7548cd7 - std::sys_common::backtrace::_print::h64d038cf8ac3e13e
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/sys_common/backtrace.rs:48:5
7: 0x5599e7548cd7 - std::sys_common::backtrace::print::h359300b4a7fccf65
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/sys_common/backtrace.rs:35:9
8: 0x5599e7548cd7 - std::panicking::default_hook::{{closure}}::hf51be35e2f510149
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:295:22
9: 0x5599e75489a0 - std::panicking::default_hook::h03ca0f22e1d2d25e
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:314:9
10: 0x5599e7549429 - std::panicking::rust_panic_with_hook::h3b7380e99b825b63
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:698:17
11: 0x5599e7549117 - std::panicking::begin_panic_handler::{{closure}}::h8e849d0710154ce0
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:588:13
12: 0x5599e75470f4 - std::sys_common::backtrace::__rust_end_short_backtrace::hedcdaddbd4c46cc5
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/sys_common/backtrace.rs:138:18
13: 0x5599e7548e29 - rust_begin_unwind
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:584:5
14: 0x5599e737dcb3 - core::panicking::panic_fmt::he1bbc7336d49a357
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/core/src/panicking.rs:143:14
15: 0x5599e737dbf2 - core::panicking::panic_bounds_check::h7777e18766a27b0b
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/core/src/panicking.rs:85:5
16: 0x5599e73a4d1f - mudskipper::query_bam_records::BAMQueryRecordReader::group_records::h3e557bbfbf98c5b3
17: 0x5599e73a55cd - mudskipper::query_bam_records::BAMQueryRecordReader::get_next_query_records::hd44f4b13b6418ce6
18: 0x5599e73946dd - mudskipper::bam::bam2bam::h107271027deeb930
19: 0x5599e739069c - mudskipper::main::hd9af9ad03c0768b5
20: 0x5599e7393d23 - std::sys_common::backtrace::__rust_begin_short_backtrace::h6d04830762f92fce
21: 0x5599e73a6249 - std::rt::lang_start::{{closure}}::h3a11e2c99d3705be
22: 0x5599e7546311 - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::hb7014f43484a8b4e
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/core/src/ops/function.rs:259:13
23: 0x5599e7546311 - std::panicking::try::do_call::h7bc9dc436daeb8c7
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:492:40
24: 0x5599e7546311 - std::panicking::try::h653d68a27ff5f175
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:456:19
25: 0x5599e7546311 - std::panic::catch_unwind::h9d739f9f59895e68
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panic.rs:137:14
26: 0x5599e7546311 - std::rt::lang_start_internal::{{closure}}::hf006f2bc7ce22bbe
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/rt.rs:128:48
27: 0x5599e7546311 - std::panicking::try::do_call::hfb39d6df61a2e69f
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:492:40
28: 0x5599e7546311 - std::panicking::try::h13e2d225134958ac
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panicking.rs:456:19
29: 0x5599e7546311 - std::panic::catch_unwind::h3bd49b5a5dfb1a50
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/panic.rs:137:14
30: 0x5599e7546311 - std::rt::lang_start_internal::h2ba92edce36c035e
at /rustc/7737e0b5c4103216d6fd8cf941b7ab9bdbaace7c/library/std/src/rt.rs:128:20
31: 0x5599e7391632 - main
32: 0x2b9c394ed555 - __libc_start_main
33: 0x5599e737e4e9 - <unknown>
34: 0x0 - <unknown>
I get the same error on a few other BAMs I've tried as well
And the same error persist if I do this
mudskipper bulk --gtf /SAN/vyplab/vyplab_reference_genomes/annotation/human/GRCh38/gencode.v40.annotation.gtf --alignment my.sorted.bam --out my.mud.bam --threads 4
Dropping some alignments against overlapping transcripts
In sample ERR188079, I have seen a case where some overlapping transcripts are dropped from the output of mudskipper. Also there is some non-deterministic behavior of mudskipper in this case.
More specifically, read HWI-ST758:71:C06LWACXX:1:1101:4517:28047 is aligned to ENST00000376420.9 and ENST00000444096.5 transcripts in one run, while aligned to ENST00000462857.5 and ENST00000495946.5 in another run. These alternative transcripts are overlapping.
The point is that if alignment to any of these is valid, we should always get all of those alignments.
assertion failure: last>=first
I am attempting to do a bulk RNA-Seq genome alignment conversion to transcriptome coordinates and keep encountering this error:
thread 'main' panicked at 'assertion failed: last >= first', /home/lkmack/.cargo/registry/src/github.com-1ecc6299db9ec823/coitrees-0.2.1/src/lib.rs:196:9
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace
I'm having a hard time figuring out if this is indicating an issue in my bam files or in my gtf file.
So far, I have checked the gtf file to ensure the start and stop coordinates are correct which they are. I have also run a second samtools sort attempt on my bam files in case this was the issue with no luck. Any pointers are appreciated.
Properly set the flag for secondary alignments
Recover cell barcode if it contains a single N only
In Salmon, there is a step for recovering barcodes that contain N's. If there is only one N, it will be replaced with A, otherwise that barcode will be ignored:
https://github.com/COMBINE-lab/salmon/blob/447ae4eef9bcf2b6293a01a99fbbd8d5007e370d/src/SalmonAlevin.cpp#L686-L694
It would be nice to implement the same logic here too.
Let the user choose the path for the GTF index
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