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Merged
merged 22 commits into from
Aug 4, 2020
Merged

Add basic functionality to read indexed FASTA files (continued) #214

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47355a3
Cherry pick the pull request for faidx
landesfeind Jun 10, 2020
4780c0c
Cargo formatting
landesfeind Jun 10, 2020
64da403
Update faidx documentation for clarification
landesfeind Jun 14, 2020
e9d2148
Implement faidx_open test
landesfeind Jun 14, 2020
4531a4d
Run actions on faidx branch
landesfeind Jun 14, 2020
29565f9
Remove faidx from github actions
landesfeind Jun 14, 2020
67d03d6
Merge branch 'master' of https://github.com/rust-bio/rust-htslib into…
landesfeind Jun 14, 2020
a29369a
Merge branch 'faidx' of github.com:landesfeind/rust-htslib into faidx
landesfeind Jun 14, 2020
79bbf8f
Activate CI for faidx branch
landesfeind Jun 14, 2020
8f7f789
update osx bindings with faidx support
pmarks Jun 16, 2020
a58680d
update linux bindings for faidx
pmarks Jun 16, 2020
bea3e9f
Drop faidx branch from CI actions
landesfeind Jun 22, 2020
16692a3
Merge remote-tracking branch 'upstream/master' into faidx
landesfeind Jun 23, 2020
78d0e84
Migrate faidx to use thiserror instead of snafu (https://github.com/r…
landesfeind Jun 23, 2020
1770a09
Use i64 in faidx and return byte array
landesfeind Jun 27, 2020
b4c265b
Formatting using cargo fmt
landesfeind Jun 27, 2020
cbab854
Merge branch 'faidx' of github.com:landesfeind/rust-htslib into faidx
landesfeind Jun 27, 2020
f735af8
Merge branch 'master' into faidx
brainstorm Jul 2, 2020
c6dc913
Use usize-type for position paramter in faidx
landesfeind Jul 18, 2020
242db0c
Merge branch 'master' into faidx
brainstorm Jul 20, 2020
ac5aa20
Correct typo in faidx-error: to -> too
landesfeind Jul 20, 2020
33dba58
Merge branch 'faidx' of github.com:landesfeind/rust-htslib into faidx
landesfeind Jul 20, 2020
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4 changes: 2 additions & 2 deletions .github/workflows/rust.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ name: CI

on:
push:
branches: [ master ]
branches: [ master, faidx ]
pull_request:
branches: [ master ]

Expand Down Expand Up @@ -104,4 +104,4 @@ jobs:
with:
use-cross: true
command: build
args: --target x86_64-unknown-linux-musl --all-features
args: --target x86_64-unknown-linux-musl --all-features
152 changes: 152 additions & 0 deletions hts-sys/linux_prebuilt_bindings.rs
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Expand Up @@ -11239,6 +11239,158 @@ fn bindgen_test_layout_kbitset_iter_t() {
)
);
}
#[repr(C)]
#[derive(Debug, Copy, Clone)]
pub struct __faidx_t {
_unused: [u8; 0],
}
pub type faidx_t = __faidx_t;
pub const fai_format_options_FAI_NONE: fai_format_options = 0;
pub const fai_format_options_FAI_FASTA: fai_format_options = 1;
pub const fai_format_options_FAI_FASTQ: fai_format_options = 2;
pub type fai_format_options = u32;
extern "C" {
pub fn fai_build3(
fn_: *const ::std::os::raw::c_char,
fnfai: *const ::std::os::raw::c_char,
fngzi: *const ::std::os::raw::c_char,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn fai_build(fn_: *const ::std::os::raw::c_char) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn fai_destroy(fai: *mut faidx_t);
}
pub const fai_load_options_FAI_CREATE: fai_load_options = 1;
pub type fai_load_options = u32;
extern "C" {
pub fn fai_load3(
fn_: *const ::std::os::raw::c_char,
fnfai: *const ::std::os::raw::c_char,
fngzi: *const ::std::os::raw::c_char,
flags: ::std::os::raw::c_int,
) -> *mut faidx_t;
}
extern "C" {
pub fn fai_load(fn_: *const ::std::os::raw::c_char) -> *mut faidx_t;
}
extern "C" {
pub fn fai_load3_format(
fn_: *const ::std::os::raw::c_char,
fnfai: *const ::std::os::raw::c_char,
fngzi: *const ::std::os::raw::c_char,
flags: ::std::os::raw::c_int,
format: fai_format_options,
) -> *mut faidx_t;
}
extern "C" {
pub fn fai_load_format(
fn_: *const ::std::os::raw::c_char,
format: fai_format_options,
) -> *mut faidx_t;
}
extern "C" {
pub fn fai_fetch(
fai: *const faidx_t,
reg: *const ::std::os::raw::c_char,
len: *mut ::std::os::raw::c_int,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn fai_fetch64(
fai: *const faidx_t,
reg: *const ::std::os::raw::c_char,
len: *mut hts_pos_t,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn fai_fetchqual(
fai: *const faidx_t,
reg: *const ::std::os::raw::c_char,
len: *mut ::std::os::raw::c_int,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn fai_fetchqual64(
fai: *const faidx_t,
reg: *const ::std::os::raw::c_char,
len: *mut hts_pos_t,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn faidx_fetch_nseq(fai: *const faidx_t) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn faidx_fetch_seq(
fai: *const faidx_t,
c_name: *const ::std::os::raw::c_char,
p_beg_i: ::std::os::raw::c_int,
p_end_i: ::std::os::raw::c_int,
len: *mut ::std::os::raw::c_int,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn faidx_fetch_seq64(
fai: *const faidx_t,
c_name: *const ::std::os::raw::c_char,
p_beg_i: hts_pos_t,
p_end_i: hts_pos_t,
len: *mut hts_pos_t,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn faidx_fetch_qual(
fai: *const faidx_t,
c_name: *const ::std::os::raw::c_char,
p_beg_i: ::std::os::raw::c_int,
p_end_i: ::std::os::raw::c_int,
len: *mut ::std::os::raw::c_int,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn faidx_fetch_qual64(
fai: *const faidx_t,
c_name: *const ::std::os::raw::c_char,
p_beg_i: hts_pos_t,
p_end_i: hts_pos_t,
len: *mut hts_pos_t,
) -> *mut ::std::os::raw::c_char;
}
extern "C" {
pub fn faidx_has_seq(
fai: *const faidx_t,
seq: *const ::std::os::raw::c_char,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn faidx_nseq(fai: *const faidx_t) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn faidx_iseq(
fai: *const faidx_t,
i: ::std::os::raw::c_int,
) -> *const ::std::os::raw::c_char;
}
extern "C" {
pub fn faidx_seq_len(
fai: *const faidx_t,
seq: *const ::std::os::raw::c_char,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn fai_parse_region(
fai: *const faidx_t,
s: *const ::std::os::raw::c_char,
tid: *mut ::std::os::raw::c_int,
beg: *mut hts_pos_t,
end: *mut hts_pos_t,
flags: ::std::os::raw::c_int,
) -> *const ::std::os::raw::c_char;
}
extern "C" {
pub fn fai_set_cache_size(fai: *mut faidx_t, cache_size: ::std::os::raw::c_int);
}
extern "C" {
#[link_name = "\u{1}wrap_kbs_init2"]
pub fn kbs_init2(ni: size_t, fill: ::std::os::raw::c_int) -> *mut kbitset_t;
Expand Down
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