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Fix compilation on aarch64 Linux #8

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Fix compilation on aarch64 Linux #8

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44 changes: 22 additions & 22 deletions src/file.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ use crate::error::{OneError, Result};
use crate::ffi;
use crate::schema::OneSchema;
use std::collections::HashMap;
use std::ffi::{CStr, CString};
use std::ffi::{CStr, CString, c_char};
use std::ptr;

// Note: The C library's errorString is now _Thread_local (patched in ONEcode/ONElib.c)
Expand Down Expand Up @@ -190,7 +190,7 @@ impl OneFile {
unsafe {
ffi::oneWriteLine(
self.ptr,
line_type as i8,
line_type as c_char,
list_len,
list_buf.unwrap_or(ptr::null_mut()),
);
Expand All @@ -203,7 +203,7 @@ impl OneFile {
unsafe {
// We need to use a format string for the variadic function
let format = CString::new("%s")?;
ffi::oneWriteComment(self.ptr, format.as_ptr() as *mut i8, c_comment.as_ptr());
ffi::oneWriteComment(self.ptr, format.as_ptr() as *mut c_char, c_comment.as_ptr());
}
Ok(())
}
Expand All @@ -222,7 +222,7 @@ impl OneFile {
self.ptr,
c_prog.as_ptr(),
c_version.as_ptr(),
format.as_ptr() as *mut i8,
format.as_ptr() as *mut c_char,
c_command.as_ptr(),
);
Ok(result)
Expand Down Expand Up @@ -265,7 +265,7 @@ impl OneFile {
unsafe {
let success = ffi::oneStats(
self.ptr,
line_type as i8,
line_type as c_char,
&mut count,
&mut max,
&mut total,
Expand All @@ -287,7 +287,7 @@ impl OneFile {
/// Setting i == 0 goes to the start of the data.
pub fn goto(&mut self, line_type: char, index: i64) -> Result<()> {
unsafe {
let success = ffi::oneGoto(self.ptr, line_type as i8, index);
let success = ffi::oneGoto(self.ptr, line_type as c_char, index);
if !success {
return Err(OneError::Other(format!(
"Failed to goto object {} of type '{}'",
Expand Down Expand Up @@ -388,7 +388,7 @@ impl OneFile {
pub fn set_char(&mut self, field: usize, value: char) {
unsafe {
let fields = (*self.ptr).field;
(*fields.add(field)).c = value as i8;
(*fields.add(field)).c = value as c_char;
}
}

Expand Down Expand Up @@ -420,7 +420,7 @@ impl OneFile {
/// Returns a reference to the string data.
pub fn string(&self) -> Option<&str> {
unsafe {
let ptr = ffi::_oneList(self.ptr) as *const i8;
let ptr = ffi::_oneList(self.ptr) as *const c_char;
if ptr.is_null() {
None
} else {
Expand Down Expand Up @@ -495,7 +495,7 @@ impl OneFile {
/// Pass the current string pointer to get the next one.
pub fn next_string<'a>(&self, current: &'a str) -> Option<&'a str> {
unsafe {
let next_ptr = current.as_ptr().add(current.len() + 1) as *const i8;
let next_ptr = current.as_ptr().add(current.len() + 1) as *const c_char;
if *next_ptr == 0 {
None
} else {
Expand Down Expand Up @@ -588,17 +588,17 @@ impl OneFile {

unsafe {
// Navigate to the FIRST 'g' group object (objects are numbered starting at 1)
if ffi::oneGoto(self.ptr, 'g' as i8, 1) {
if ffi::oneGoto(self.ptr, 'g' as c_char, 1) {
let mut contig_id = 0i64;
let mut current_scaffold_name = String::new();
let mut is_first_line = true;

loop {
let line_type = ffi::oneReadLine(self.ptr) as u8 as char;
if line_type == '\0' {
break; // EOF
}

match line_type {
'S' => {
// New scaffold - store its name
Expand Down Expand Up @@ -647,7 +647,7 @@ impl OneFile {
let saved_line = self.line_number();

unsafe {
if ffi::oneGoto(self.ptr, 'g' as i8, 1) {
if ffi::oneGoto(self.ptr, 'g' as c_char, 1) {
let mut group_contig_id = 0i64; // Per-group contig ID (resets for each 'g')
let mut current_group_names = HashMap::new();
let mut current_group_lengths = HashMap::new();
Expand Down Expand Up @@ -760,7 +760,7 @@ impl OneFile {
// First, count contigs in all previous groups to get the starting contig_id
let mut starting_contig_id = 0i64;
for prev_group in 1..group_num {
if ffi::oneGoto(self.ptr, 'g' as i8, prev_group) {
if ffi::oneGoto(self.ptr, 'g' as c_char, prev_group) {
loop {
let line_type = ffi::oneReadLine(self.ptr) as u8 as char;
if line_type == '\0' || line_type == 'g' || line_type == 'A' || line_type == 'a' {
Expand All @@ -774,7 +774,7 @@ impl OneFile {
}

// Now read the target group with correct starting ID
if ffi::oneGoto(self.ptr, 'g' as i8, group_num) {
if ffi::oneGoto(self.ptr, 'g' as c_char, group_num) {
let mut contig_id = starting_contig_id;
let mut current_scaffold_name = String::new();
let mut is_first_line = true;
Expand Down Expand Up @@ -824,7 +824,7 @@ impl OneFile {

unsafe {
// Navigate to the first 'g' group object (GDB skeleton)
if ffi::oneGoto(self.ptr, 'g' as i8, 1) {
if ffi::oneGoto(self.ptr, 'g' as c_char, 1) {
let mut contig_id = 0i64;
let mut current_scaffold_name = String::new();
let mut is_first_line = true;
Expand Down Expand Up @@ -888,7 +888,7 @@ impl OneFile {
// Count contigs in previous groups
let mut starting_contig_id = 0i64;
for prev_group in 1..group_num {
if ffi::oneGoto(self.ptr, 'g' as i8, prev_group) {
if ffi::oneGoto(self.ptr, 'g' as c_char, prev_group) {
loop {
let line_type = ffi::oneReadLine(self.ptr) as u8 as char;
if line_type == '\0' || line_type == 'g' || line_type == 'A' || line_type == 'a' {
Expand All @@ -902,7 +902,7 @@ impl OneFile {
}

// Read target group
if ffi::oneGoto(self.ptr, 'g' as i8, group_num) {
if ffi::oneGoto(self.ptr, 'g' as c_char, group_num) {
let mut contig_id = starting_contig_id;
let mut current_scaffold_length = 0i64;
let mut scaffold_contigs = Vec::new();
Expand Down Expand Up @@ -970,7 +970,7 @@ impl OneFile {
// Count contigs in previous groups
let mut starting_contig_id = 0i64;
for prev_group in 1..group_num {
if ffi::oneGoto(self.ptr, 'g' as i8, prev_group) {
if ffi::oneGoto(self.ptr, 'g' as c_char, prev_group) {
loop {
let line_type = ffi::oneReadLine(self.ptr) as u8 as char;
if line_type == '\0' || line_type == 'g' || line_type == 'A' || line_type == 'a' {
Expand All @@ -984,7 +984,7 @@ impl OneFile {
}

// Read target group
if ffi::oneGoto(self.ptr, 'g' as i8, group_num) {
if ffi::oneGoto(self.ptr, 'g' as c_char, group_num) {
let mut contig_id = starting_contig_id;
let mut spos = 0i64;
let mut is_first_line = true;
Expand Down Expand Up @@ -1036,7 +1036,7 @@ impl OneFile {
let saved_line = self.line_number();

unsafe {
if ffi::oneGoto(self.ptr, 'g' as i8, 1) {
if ffi::oneGoto(self.ptr, 'g' as c_char, 1) {
let mut contig_id = 0i64;
let mut current_scaffold_length = 0i64;
let mut scaffold_contigs = Vec::new(); // Track contigs in current scaffold
Expand Down Expand Up @@ -1128,7 +1128,7 @@ impl OneFile {

// Navigate to the FIRST 'g' group object (GDB skeleton)
unsafe {
if ffi::oneGoto(self.ptr, 'g' as i8, 1) {
if ffi::oneGoto(self.ptr, 'g' as c_char, 1) {
let mut contig_id = 0i64;
let mut spos = 0i64; // scaffold position accumulator
let mut is_first_line = true;
Expand Down