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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
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Release 1.4.2/1.5.0 #136

Open martin-g opened 1 year ago

martin-g commented 1 year ago

Hello,

I'd like to request a new release because v1.4.1 cannot be built on aarch64 architecture due to:

11:24:43 BIOCONDA INFO (OUT) error[E0308]: mismatched types
11:24:43 BIOCONDA INFO (OUT)    --> /opt/conda/conda-bld/10x_bamtofastq_1681816419021/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:152:16
11:24:43 BIOCONDA INFO (OUT)     |
11:24:43 BIOCONDA INFO (OUT) 152 |             s: sam_copy.as_ptr() as *mut i8,
11:24:43 BIOCONDA INFO (OUT)     |                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
11:24:43 BIOCONDA INFO (OUT)     |
11:24:43 BIOCONDA INFO (OUT)     = note: expected raw pointer `*mut u8`
11:24:43 BIOCONDA INFO (OUT)                found raw pointer `*mut i8`
11:24:43 BIOCONDA INFO (OUT) 
11:24:43 BIOCONDA INFO (OUT) error[E0308]: mismatched types
11:24:43 BIOCONDA INFO (OUT)     --> /opt/conda/conda-bld/10x_bamtofastq_1681816419021/_build_env/.cargo/registry/src/github.com-1ecc6299db9ec823/rust-htslib-0.38.2/src/bam/record.rs:583:17
11:24:43 BIOCONDA INFO (OUT)      |
11:24:43 BIOCONDA INFO (OUT) 581  |             htslib::bam_aux_get(
11:24:43 BIOCONDA INFO (OUT)      |             ------------------- arguments to this function are incorrect
11:24:43 BIOCONDA INFO (OUT) 582  |                 &self.inner as *const htslib::bam1_t,
11:24:43 BIOCONDA INFO (OUT) 583  |                 c_str.as_ptr() as *mut i8,
11:24:43 BIOCONDA INFO (OUT)      |                 ^^^^^^^^^^^^^^^^^^^^^^^^^ expected `u8`, found `i8`
11:24:43 BIOCONDA INFO (OUT)      |
11:24:43 BIOCONDA INFO (OUT)      = note: expected raw pointer `*const u8`
11:24:43 BIOCONDA INFO (OUT)                 found raw pointer `*mut i8`

The problem has been fixed in rust-htslib 0.39.3 with https://github.com/rust-bio/rust-htslib/commit/a21aff289bc03c7549afc7a958084ed57e8c93f2

bamtofastq already depends on 0.42 - https://github.com/10XGenomics/bamtofastq/blob/8720dcd0bf39ef9ed9f40054d6c136f7ce9eb37d/Cargo.toml#L21

martin-g commented 1 year ago

I've just tested latest master on openEuler Linux ARM64 and everything is OK:

❯ cargo build
    Updating crates.io index
  Downloaded either v1.8.1
  Downloaded proc-macro2 v1.0.52
  Downloaded serde v1.0.156
  Downloaded tinyvec_macros v0.1.1
  Downloaded regex-syntax v0.6.29
  Downloaded heck v0.4.1
  Downloaded rustversion v1.0.12
  Downloaded ieee754 v0.2.6
  Downloaded thiserror-impl v1.0.39
  Downloaded serde_bytes v0.11.9
  Downloaded io-lifetimes v1.0.4
  Downloaded flate2 v1.0.25
  Downloaded quick-error v1.2.3
  Downloaded bincode v1.3.3
  Downloaded cmake v0.1.49
  Downloaded aho-corasick v0.7.20
  Downloaded regex v1.7.3
  Downloaded fastrand v1.9.0
  Downloaded itoa v1.0.6
  Downloaded custom_derive v0.1.7
  Downloaded quote v1.0.26
  Downloaded derive-new v0.5.9
  Downloaded jobserver v0.1.26
  Downloaded rustc-demangle v0.1.21
  Downloaded thiserror v1.0.39
  Downloaded glob v0.3.1
  Downloaded min-max-heap v1.3.0
  Downloaded addr2line v0.19.0
  Downloaded ryu v1.0.13
  Downloaded crossbeam-utils v0.8.15
  Downloaded tempfile v3.5.0
  Downloaded docopt v1.1.1
  Downloaded serde_derive v1.0.156
  Downloaded anyhow v1.0.70
  Downloaded unicode-ident v1.0.8
  Downloaded miniz_oxide v0.6.2
  Downloaded backtrace v0.3.67
  Downloaded cc v1.0.79
  Downloaded unicode-bidi v0.3.13
  Downloaded crossbeam-channel v0.5.7
  Downloaded syn v1.0.109
  Downloaded object v0.30.3
  Downloaded rustix v0.37.7
  Downloaded libc v0.2.140
  Downloaded gimli v0.27.2
  Downloaded lzma-sys v0.1.20
  Downloaded semver v0.1.20
  Downloaded rustc_version v0.1.7
  Downloaded linear-map v1.2.0
  Downloaded newtype_derive v0.1.6
  Downloaded shardio v0.8.2
  Downloaded rust-htslib v0.42.0
  Downloaded libdeflate-sys v0.7.5
  Downloaded bio-types v0.13.0
  Downloaded fs-utils v1.1.4
  Downloaded linux-raw-sys v0.3.1
  Downloaded csv v1.2.1
  Downloaded hts-sys v2.0.3
  Downloaded 58 crates (11.7 MB) in 8.04s (largest was `hts-sys` at 4.7 MB)
   Compiling libc v0.2.140
   Compiling proc-macro2 v1.0.52
   Compiling quote v1.0.26
   Compiling unicode-ident v1.0.8
   Compiling syn v1.0.109
   Compiling memchr v2.5.0
   Compiling pkg-config v0.3.26
   Compiling cfg-if v1.0.0
   Compiling serde_derive v1.0.156
   Compiling serde v1.0.156
   Compiling tinyvec_macros v0.1.1
   Compiling semver v0.1.20
   Compiling quick-error v1.2.3
   Compiling rustversion v1.0.12
   Compiling thiserror v1.0.39
   Compiling io-lifetimes v1.0.4
   Compiling crossbeam-utils v0.8.15
   Compiling adler v1.0.2
   Compiling regex-syntax v0.6.29
   Compiling glob v0.3.1
   Compiling gimli v0.27.2
   Compiling rustc-demangle v0.1.21
   Compiling lazy_static v1.4.0
   Compiling crc32fast v1.3.2
   Compiling anyhow v1.0.70
   Compiling log v0.4.17
   Compiling rustix v0.37.7
   Compiling heck v0.4.1
   Compiling percent-encoding v2.2.0
   Compiling unicode-bidi v0.3.13
   Compiling bitflags v1.3.2
   Compiling byteorder v1.4.3
   Compiling linux-raw-sys v0.3.1
   Compiling itoa v1.0.6
   Compiling ryu v1.0.13
   Compiling ieee754 v0.2.6
   Compiling linear-map v1.2.0
   Compiling fastrand v1.9.0
   Compiling either v1.8.1
   Compiling strsim v0.10.0
   Compiling min-max-heap v1.3.0
   Compiling custom_derive v0.1.7
   Compiling tinyvec v1.6.0
   Compiling fs-utils v1.1.4
   Compiling miniz_oxide v0.6.2
   Compiling rustc_version v0.1.7
   Compiling form_urlencoded v1.1.0
   Compiling itertools v0.10.5
   Compiling newtype_derive v0.1.6
   Compiling addr2line v0.19.0
   Compiling unicode-normalization v0.1.22
   Compiling aho-corasick v0.7.20
   Compiling object v0.30.3
   Compiling csv-core v0.1.10
   Compiling jobserver v0.1.26
   Compiling crossbeam-channel v0.5.7
   Compiling idna v0.3.0
   Compiling regex v1.7.3
   Compiling cc v1.0.79
   Compiling url v2.3.1
   Compiling cmake v0.1.49
   Compiling libdeflate-sys v0.7.5
   Compiling bzip2-sys v0.1.11+1.0.8
   Compiling lzma-sys v0.1.20
   Compiling backtrace v0.3.67
   Compiling lz4-sys v1.9.4
   Compiling hts-sys v2.0.3
   Compiling libz-sys v1.1.8
   Compiling tempfile v3.5.0
   Compiling thiserror-impl v1.0.39
   Compiling derive-new v0.5.9
   Compiling strum_macros v0.24.3
   Compiling bio-types v0.13.0
   Compiling lz4 v1.24.0
   Compiling flate2 v1.0.25
   Compiling bincode v1.3.3
   Compiling docopt v1.1.1
   Compiling serde_bytes v0.11.9
   Compiling csv v1.2.1
   Compiling shardio v0.8.2
   Compiling rust-htslib v0.42.0
   Compiling bamtofastq v1.4.1 (/home/mgrigorov/git/bamtofastq)
    Finished dev [optimized + debuginfo] target(s) in 3m 36s

❯ cargo test
   Compiling bamtofastq v1.4.1 (/home/mgrigorov/git/bamtofastq)
    Finished test [optimized + debuginfo] target(s) in 11.39s
     Running unittests src/main.rs (target/debug/deps/bamtofastq-972c99a3bf824d2c)

running 7 tests
test tests::bad_bam ... ok
test tests::wrong_header ... ok
test tests::unpaired_record ... ok
test tests::test_cr12 ... ok
test tests::test_lr20 ... ok
test tests::test_lr21 ... ok
test tests::test_cr12_v1 ... ok

test result: ok. 7 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.16s