From 0b312a9ce04b64516b32d42b1a72d52b9ac3c27b Mon Sep 17 00:00:00 2001
From: Daniel Baker <dbaker@pacificbiosciences.com>
Date: Thu, 28 Sep 2023 13:05:44 -0700
Subject: [PATCH] Add rust_htslib::bcf::index::build, to build a bcf/vcf index.

---
 src/bcf/index.rs | 71 ++++++++++++++++++++++++++++++++++++++++++++++++
 src/bcf/mod.rs   |  1 +
 2 files changed, 72 insertions(+)
 create mode 100644 src/bcf/index.rs

diff --git a/src/bcf/index.rs b/src/bcf/index.rs
new file mode 100644
index 000000000..9c548a5a1
--- /dev/null
+++ b/src/bcf/index.rs
@@ -0,0 +1,71 @@
+use crate::{htslib, utils};
+
+#[derive(Debug)]
+pub struct BcfBuildError {
+    pub msg: String,
+}
+
+/// Index type to build.
+pub enum Type {
+    /// Tabix index
+    Tbx,
+    /// CSI index, with given minimum shift
+    Csi(u32),
+}
+
+impl Type {
+    fn min_shift(&self) -> i32 {
+        match self {
+            Self::Tbx => 0,
+            Self::Csi(x) => *x as i32,
+        }
+    }
+}
+
+impl BcfBuildError {
+    pub fn error_message(error: i32) -> &'static str {
+        match error {
+            -1 => "indexing failed",
+            -2 => "opening @fn failed",
+            -3 => "format not indexable",
+            -4 => "failed to create and/or save the index",
+            _ => "unknown error",
+        }
+    }
+}
+impl std::error::Error for BcfBuildError {}
+
+impl std::fmt::Display for BcfBuildError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        write!(f, "BcfBuildError{{msg: {}}}", self.msg)
+    }
+}
+
+/// Build a bcf or vcf.gz index.
+/// Builds tbi or csi depending on index_type.
+pub fn build<P: AsRef<std::path::Path>>(
+    bcf_path: P,
+    idx_path: Option<P>,
+    n_threads: u32,
+    index_type: Type,
+) -> Result<(), BcfBuildError> {
+    let min_shift = index_type.min_shift();
+    let idx_path_cstr = idx_path.map(|p| utils::path_to_cstring(&p).expect("path_to_cstring"));
+    let ret = unsafe {
+        htslib::bcf_index_build3(
+            utils::path_to_cstring(&bcf_path).unwrap().as_ptr(),
+            idx_path_cstr.map_or(std::ptr::null(), |p| p.as_ptr()),
+            min_shift,
+            n_threads as i32,
+        )
+    };
+    match ret {
+        0 => Ok(()),
+        e => Err(BcfBuildError {
+            msg: format!(
+                "Failed to build  bcf index. Error: {e:?}/{}",
+                BcfBuildError::error_message(e)
+            ),
+        }),
+    }
+}
diff --git a/src/bcf/mod.rs b/src/bcf/mod.rs
index 7669911be..ab10dec0d 100644
--- a/src/bcf/mod.rs
+++ b/src/bcf/mod.rs
@@ -112,6 +112,7 @@ use url::Url;
 
 pub mod buffer;
 pub mod header;
+pub mod index;
 pub mod record;
 
 use crate::bcf::header::{HeaderView, SampleSubset};