Merge pull request #4 from alejandrogzi/lex_algorithm

Pre-sorting using a lexicograph-based algorithm
alejandrogzi · Oct 17, 2023 · 1c974ed · 1c974ed
2 parents 57b3952 + 7d1141e
commit 1c974ed
Show file tree

Hide file tree

Showing 8 changed files with 675 additions and 187 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "bed2gtf"
-version = "1.6.0"
+version = "1.7.0"
 authors = ["alejandrogzi <jose.gonzalesdezavala1@unmsm.edu.pe>"]
 edition = "2021"
 license = "MIT"
@@ -18,6 +18,9 @@ peak_alloc = {version = "0.2.0"}
 log = "0.4.14"
 simple_logger = "4.0.0"
 indoc = "1.0"
+natord = "1.0.9"
+thiserror = "1.0"
+chrono = "0.4.31"
 
 [profile.release]
 lto = true

diff --git a/README.md b/README.md
@@ -21,6 +21,11 @@ chr27 bed2gtf exon 17266470 17266572 . + . gene_id "ENSG00000151743"; transcript
 
 in a few seconds.
 
+>[!IMPORTANT]
+>
+>Now bed2gtf uses a lexicograph-based algorithm to offer the user not only a .gtf file but a nicely sorted .gtf file. The algorithm was originally implemented in [gtfsort](https://github.com/alejandrogzi/gtfsort), and some parts have been coupled with bed2gtf code. 
+
+
 ## Usage
 ``` rust
 Usage: bed2gtf[EXE] --bed <BED> --isoforms <ISOFORMS> --output <OUTPUT>
@@ -161,8 +166,7 @@ bed2gtf is basically the reimplementation of C binaries merged in 1 step. This t
 ### Limitations
 At the time of bed2gtf being publicly available some gaps have not been covered yet. 
 
-1. By the last release of bed2gtf (1.5.0) a novel GTF sorting tool have benn already developed, covering one of the past limitations of bed2gtf, the tool resides here: [gtfsort](https://github.com/alejandrogzi/gtfsort)
-2. Biotype. As you may know (or not), GTF files specify the gene_biotype of each entry (e.g. protein_coding, processed_pseudogene, snoRNA, etc). This is probably the biggest limitation in this release. Currently, bed2gtf DOES NOT assume any biotype. In future releases will probably be an option to specify the gene_biotype [-b/--biotype] or maybe be included in the isoforms file.
+1. Biotype. As you may know (or not), GTF files specify the gene_biotype of each entry (e.g. protein_coding, processed_pseudogene, snoRNA, etc). This is probably the biggest limitation in this release. Currently, bed2gtf DOES NOT assume any biotype. In future releases will probably be an option to specify the gene_biotype [-b/--biotype] or maybe be included in the isoforms file.
 
 ### Annex