From ee32dc617ba81725eece4ec3b8f5ca21ac35a219 Mon Sep 17 00:00:00 2001
From: Kai Zhang <zhangkai33@westlake.edu.cn>
Date: Wed, 2 Oct 2024 21:46:35 +0800
Subject: [PATCH] minor

---
 README.md                     |  5 +++++
 docs/_static/versions.json    |  4 ++--
 docs/tutorials/index.rst      |  1 +
 docs/tutorials/txg_atac.ipynb |  3 +++
 python/Cargo.toml             |  2 +-
 python/src/pyseqspec.rs       | 19 ++++++++++---------
 6 files changed, 22 insertions(+), 12 deletions(-)
 create mode 100644 docs/tutorials/txg_atac.ipynb

diff --git a/README.md b/README.md
index ccbbd36..1d2bb32 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,10 @@
 # Single-cell genomics preprocessing package
 
+![PyPI](https://img.shields.io/pypi/v/precellar)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/precellar)
+![Continuous integration](https://github.com/regulatory-genomics/precellar/workflows/test-python-package/badge.svg)
+![GitHub Repo stars](https://img.shields.io/github/stars/regulatory-genomics/precellar?style=social)
+
 This tool is an automated pipeline for preprocessing single-cell genomics data.
 It is designed to take raw data (fastq files) from a variety of single-cell genomics
 platforms and a seqspec file as input, and output a count matrix (RNA) or a fragment file (ATAC)
diff --git a/docs/_static/versions.json b/docs/_static/versions.json
index dc99f0f..4d40cca 100644
--- a/docs/_static/versions.json
+++ b/docs/_static/versions.json
@@ -6,8 +6,8 @@
     },
     {
         "name": "0.1 (stable)",
-        "version": "dev",
+        "version": "0.1",
         "preferred": true,
-        "url": "https://lab.kaizhang.org/precellar/version/dev/"
+        "url": "https://lab.kaizhang.org/precellar/version/0.1/"
     }
 ]
\ No newline at end of file
diff --git a/docs/tutorials/index.rst b/docs/tutorials/index.rst
index 9eda9a3..143f3cf 100644
--- a/docs/tutorials/index.rst
+++ b/docs/tutorials/index.rst
@@ -6,4 +6,5 @@
    :maxdepth: 2
 
    txg_multiome
+   txg_atac
    generic
\ No newline at end of file
diff --git a/docs/tutorials/txg_atac.ipynb b/docs/tutorials/txg_atac.ipynb
new file mode 100644
index 0000000..cf19e62
--- /dev/null
+++ b/docs/tutorials/txg_atac.ipynb
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:302d786be3973d47e4cafacfc099fc42bb1aa4440dc051f09dc23981cfaf0b0f
+size 4038562
diff --git a/python/Cargo.toml b/python/Cargo.toml
index e330fe6..df9f06d 100644
--- a/python/Cargo.toml
+++ b/python/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "precellar-py"
-version = "0.1.0"
+version = "0.1.1-dev1"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
diff --git a/python/src/pyseqspec.rs b/python/src/pyseqspec.rs
index 9b42467..e76570b 100644
--- a/python/src/pyseqspec.rs
+++ b/python/src/pyseqspec.rs
@@ -79,11 +79,11 @@ impl SeqSpec {
         min_len: Option<usize>,
         max_len: Option<usize>,
     ) -> Result<()> {
-        let mut all_reads = self.0.sequence_spec.take().unwrap_or(Vec::new());
+        let all_reads = &mut self.0.sequence_spec;
         let mut read_exist = false;
         let mut read_buffer = Read::default();
         read_buffer.read_id = read_id.to_string();
-        let read = if let Some(r) = all_reads.iter_mut().find(|r| r.read_id == read_id) {
+        let read = if let Some(r) = all_reads.as_mut().map(|r| r.iter_mut().find(|r| r.read_id == read_id)).flatten() {
             read_exist = true;
             r
         } else {
@@ -124,9 +124,12 @@ impl SeqSpec {
         }
 
         if !read_exist {
-            all_reads.push(read_buffer);
+            if let Some(r) = all_reads.as_mut() {
+                r.push(read_buffer);
+            } else {
+                all_reads.replace(vec![read_buffer]);
+            }
         }
-        self.0.sequence_spec = Some(all_reads);
 
         Ok(())
     }
@@ -208,11 +211,9 @@ fn format_read(read: &Read) -> String {
     } else {
         format!("{}-{}", read.min_len, read.max_len)
     };
-    if read.is_reverse() {
-        format!("↑{}({})", read.read_id, len)
-    } else {
-        format!("↓{}({})", read.read_id, len)
-    }
+    let orientation = if read.is_reverse() { "↑" } else { "↓" };
+    let has_files = if read.files.as_ref().map(|x| !x.is_empty()).unwrap_or(false) { "✓" } else { "✗" };
+    format!("{}{}({}){}", orientation, read.read_id, len, has_files)
 }
 
 fn make_file_path(path: &str) -> Result<File> {