cleanup reheader

COMBINE-lab · Mar 8, 2024 · 031fa2e · 031fa2e
1 parent 3fa0c86
commit 031fa2e
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Showing 17 changed files with 79 additions and 41 deletions.
diff --git a/scripts/bsd-3.tmpl b/scripts/bsd-3.tmpl
@@ -0,0 +1,6 @@
+Copyright (c) ${years} ${owner}.
+
+This file is part of ${projectname}
+(see ${projecturl}).
+
+License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
diff --git a/scripts/reheader.sh b/scripts/reheader.sh
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+if ! command -v licenseheaders &> /dev/null
+then
+    echo "licenseheaders could not be found; please install this program to use the script (pip install licenseheaders)."
+    exit 1
+fi
+
+
+licenseheaders -d ../src -y 2020-2024 -t bsd-3.tmpl -o COMBINE-lab -n alevin-fry -u https://www.github.com/COMBINE-lab/alevin-fry -D -E rs
diff --git a/src/cellfilter.rs b/src/cellfilter.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/cmd_parse_utils.rs b/src/cmd_parse_utils.rs
@@ -1,3 +1,11 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
 use crate::quant::{ResolutionStrategy, SplicedAmbiguityModel};
 use clap;
 use std::path::{Path, PathBuf};

diff --git a/src/collate.rs b/src/collate.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/constants.rs b/src/constants.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/convert.rs b/src/convert.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */
@@ -542,19 +542,7 @@ where
     let mut br = BufReader::new(i_file);
     let prelude = RadPrelude::from_bytes(&mut br)?;
     let hdr = &prelude.hdr;
-    // info!(
-    //     log,
-    //     "paired : {:?}, ref_count : {}, num_chunks : {}",
-    //     hdr.is_paired != 0,
-    //     hdr.ref_count.to_formatted_string(&Locale::en),
-    //     hdr.num_chunks.to_formatted_string(&Locale::en)
-    // );
-    // file-level
-    //let _fl_tags = rad_types::TagSection::from_bytes(&mut br);
-    // info!(log, "read {:?} file-level tags", fl_tags.tags.len());
-    // read-level
     let rl_tags = &prelude.read_tags;
-    // info!(log, "read {:?} read-level tags", rl_tags.tags.len());
 
     // right now, we only handle BC and UMI types of U8—U64, so validate that
     const BNAME: &str = "b";
@@ -585,10 +573,6 @@ where
     assert!(bct.is_some(), "barcode type tag was missing!");
     assert!(umit.is_some(), "umi type tag was missing!");
 
-    // alignment-level
-    // let _al_tags = rad_types::TagSection::from_bytes(&mut br);
-    // info!(log, "read {:?} alignemnt-level tags", al_tags.tags.len());
-
     let file_tag_map = prelude.file_tags.parse_tags_from_bytes(&mut br)?;
     info!(log, "File-level tag map {:?}", file_tag_map);
 
@@ -633,7 +617,7 @@ where
                     handle,
                     "ID:{}\tHI:{}\tNH:{}\tCB:{}\tUMI:{}\tDIR:{:?}\t{}",
                     id,
-                    i,
+                    i + 1,
                     num_entries,
                     unsafe { std::str::from_utf8_unchecked(&bitmer_to_bytes(bc_mer)[..]) },
                     unsafe { std::str::from_utf8_unchecked(&bitmer_to_bytes(umi_mer)[..]) },
@@ -649,10 +633,6 @@ where
                         return Ok(num_reads);
                     }
                 };
-
-                // writeln!(handle,"{:?}\t{:?}\t{:?}\t{:?}",
-                // bc,umi,read.dirs[i],
-                // str::from_utf8(&tid_),);
             }
             id += 1;
         }

diff --git a/src/em.rs b/src/em.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/eq_class.rs b/src/eq_class.rs
@@ -1,3 +1,11 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
 use std::collections::HashMap;
 use std::hash::{BuildHasher, Hasher};
 use std::io::BufRead;

diff --git a/src/infer.rs b/src/infer.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/io_utils.rs b/src/io_utils.rs
@@ -1,3 +1,12 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
+
 /// some (hopefully) generally useful I/O related utilities
 use anyhow::Context;
 use crossbeam_queue::ArrayQueue;

diff --git a/src/lib.rs b/src/lib.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/main.rs b/src/main.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2024 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/prog_opts.rs b/src/prog_opts.rs
@@ -1,3 +1,12 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
+
 //use derive_builder::Builder;
 use bio_types::strand::Strand;
 use serde::Serialize;

diff --git a/src/pugutils.rs b/src/pugutils.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/quant.rs b/src/quant.rs
@@ -1,8 +1,8 @@
 /*
- * Copyright (c) 2020-2022 Rob Patro, Avi Srivastava, Hirak Sarkar, Dongze He, Mohsen Zakeri.
+ * Copyright (c) 2020-2024 COMBINE-lab.
  *
  * This file is part of alevin-fry
- * (see https://github.com/COMBINE-lab/alevin-fry).
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
  *
  * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
  */

diff --git a/src/utils.rs b/src/utils.rs
@@ -1,3 +1,11 @@
+/*
+ * Copyright (c) 2020-2024 COMBINE-lab.
+ *
+ * This file is part of alevin-fry
+ * (see https://www.github.com/COMBINE-lab/alevin-fry).
+ *
+ * License: 3-clause BSD, see https://opensource.org/licenses/BSD-3-Clause
+ */
 use crate::constants as afconst;
 use crate::eq_class::IndexedEqList;
 use anyhow::{anyhow, Context};