From 929b196e3e1452000585846b25fb779159980ead Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Mon, 6 Jan 2025 10:30:52 -0800
Subject: [PATCH] debugging empty output file
---
src/sniff.rs | 40 ++++++++++++++++++++++++++++++----------
src/writer.rs | 5 +++++
2 files changed, 35 insertions(+), 10 deletions(-)
diff --git a/src/sniff.rs b/src/sniff.rs
index cf4a702..10722ae 100644
--- a/src/sniff.rs
+++ b/src/sniff.rs
@@ -2,7 +2,7 @@ use bio::io::bed;
use rust_htslib::bcf;
pub(crate) use rust_htslib::htslib as hts;
use std::fmt;
-use std::io;
+use std::io::{self, Write};
use std::mem;
use std::path::Path;
use std::rc::Rc;
@@ -79,25 +79,45 @@ impl io::Read for HtsFile {
impl io::Write for HtsFile {
fn write(&mut self, buf: &[u8]) -> io::Result<usize> {
- eprintln!("writing!, bgzf: {}", self.fh.is_bgzf());
- assert!(self.fh.is_write() != 0);
+ eprintln!("Writing {} bytes", buf.len());
+ assert!(self.fh.is_write() != 0, "File not opened for writing!");
+ assert!(self.is_bgzf(), "File is not BGZF!");
+
+ // Ensure we have data to write
+ if buf.is_empty() {
+ return Ok(0);
+ }
+
+ // Get a direct pointer to the BGZF structure
+ let bgzf = unsafe { self.fh.fp.bgzf };
+
+ // Write the buffer using a direct pointer to the data
let n = unsafe {
hts::bgzf_write(
- self.fh.fp.bgzf as *mut _,
- buf.as_ptr() as *const std::os::raw::c_void,
+ bgzf,
+ buf.as_ptr() as *const _, // Simplified pointer cast
buf.len(),
)
};
+ eprintln!("bgzf_write returned {}", n);
+
if n < 0 {
return Err(io::Error::last_os_error());
}
- unsafe { hts::hts_flush(&mut self.fh) };
- eprintln!("wrote {} bytes", n);
+
Ok(n as usize)
}
fn flush(&mut self) -> io::Result<()> {
- match unsafe { hts::hts_flush(&mut self.fh) } {
+ if self.is_bgzf() {
+ let c = unsafe { hts::bgzf_flush(self.fh.fp.bgzf as *mut _) };
+ if c < 0 {
+ return Err(io::Error::last_os_error());
+ }
+ }
+
+ let result = unsafe { hts::hts_flush(&mut self.fh) };
+ match result {
0 => Ok(()),
_ => Err(io::Error::last_os_error()),
}
@@ -106,8 +126,7 @@ impl io::Write for HtsFile {
impl Drop for HtsFile {
fn drop(&mut self) {
- eprintln!("dropping htsfile :{:?}", self);
- unsafe { hts::hts_flush(&mut self.fh) };
+ self.flush().expect("Failed to flush htsfile");
}
}
@@ -138,6 +157,7 @@ impl HtsFile {
}
pub fn new(path: &Path, mode: &str) -> io::Result<Self> {
+ eprintln!("opening file: {:?} with mode: {}", path, mode);
open(path, mode)
}
diff --git a/src/writer.rs b/src/writer.rs
index 7ce71ee..30071c8 100644
--- a/src/writer.rs
+++ b/src/writer.rs
@@ -147,6 +147,7 @@ impl Writer {
hts::htsCompression_bgzf => "wz",
_ => "w",
};
+ eprintln!("open file: {:?} with mode: {}", path, write_mode);
let hf = HtsFile::new(path.as_ref(), write_mode)
.map_err(|e| FormatConversionError::HtslibError(e.to_string()))?;
let bed_writer = bio::io::bed::Writer::new(hf);
@@ -210,6 +211,9 @@ impl Writer {
report: &Report,
crs: &[Box<dyn ColumnReporter>],
) -> Result<(), std::io::Error> {
+ if report.len() == 0 {
+ return Ok(());
+ }
match self.format {
hts::htsExactFormat_vcf => {
let vcf_writer = match &mut self.writer {
@@ -264,6 +268,7 @@ impl Writer {
}
}
hts::htsExactFormat_bed => {
+ eprintln!("report: {:?}", report);
for fragment in report {
// return an error if fragment.a is None
let frag_a = fragment.a.as_ref().ok_or_else(|| {