Prepare for v0.1.0 release

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bamrescue"
-version = "0.0.2-dev"
+version = "0.1.0"
 description = "Utility to check Binary Sequence Alignment / Map (BAM) files for corruption and repair them"
 
 authors = ["Jérémie Roquet <[email protected]>"]

README.md

@@ -51,28 +51,6 @@ Even though most tools would gave up on this file, it still contains almost
 100% of non-corrupted bam payload, and the user probably wouldn't mind much if
 they could work only on that close-to-100% amount of data.
 
-Let's rescue the non-corrupted payload (beware: this takes as much additional
-space on the disk as the original file):
-
-    $ bamrescue rescue samples/corrupted_payload.bam rescued_file.bam
-
-The output is the following:
-
-    Jun 17 23:06:48.840 INFO Rescuing data from samples/corrupted_payload.bam…
-    bam rescue statistics:
-       1870 bgzf blocks found (117 MiB of bam payload)
-          2 corrupted blocks removed (0% of total)
-         46 KiB of bam payload lost (0% of total)
-       1868 non-corrupted blocks rescued (almost 100% of total)
-        111 MiB of bam payload rescued (almost 100% of total)
-    Jun 17 23:07:10.555 ERRO INFO Data rescued to rescued_file.bam
-
-The resulting bam file can now be used like if it never had been corrupted.
-Rescued data is validated using a CRC32 checksum, so it's not like ignoring
-errors and working on corrupted data (typical use of gzip to get garbage data
-from a corrupted bam file): it's working on (ridiculously) less, validated
-data.
-
 ## Performance
 
 bamrescue is very fast. Actually, it is even faster than gzip while doing more.
@@ -132,17 +110,14 @@ Copy the `bamrescue` binary wherever you want.
 
 ```console
 Usage: bamrescue check [--quiet] [--threads=<threads>] <bamfile>
-       bamrescue rescue <bamfile> <output>
        bamrescue -h | --help
        bamrescue --version
 
 Commands:
     check                Check BAM file for corruption.
-    rescue               Keep only non-corrupted blocks of BAM file.
 
 Arguments:
     bamfile              BAM file to check or rescue.
-    output               Rescued BAM file.
 
 Options:
     -h, --help           Show this screen.

src/main.rs

@@ -17,17 +17,14 @@ use std::process;
 
 const USAGE: &str = "
 Usage: bamrescue check [--quiet] [--threads=<threads>] <bamfile>
-       bamrescue rescue <bamfile> <output>
        bamrescue -h | --help
        bamrescue --version
 
 Commands:
     check                Check BAM file for corruption.
-    rescue               Keep only non-corrupted blocks of BAM file.
 
 Arguments:
     bamfile              BAM file to check or rescue.
-    output               Rescued BAM file.
 
 Options:
     -h, --help           Show this screen.
@@ -39,9 +36,7 @@ Options:
 #[derive(RustcDecodable)]
 struct Args {
     cmd_check: bool,
-    cmd_rescue: bool,
     arg_bamfile: String,
-    arg_output: String,
     flag_quiet: bool,
     flag_threads: usize,
     flag_version: bool,
@@ -97,15 +92,5 @@ fn main() {
            results.truncated_between_blocks {
             process::exit(1);
         }
-    } else if args.cmd_rescue {
-        File::open(&args.arg_bamfile).and_then(|bamfile| {
-            File::create(&args.arg_output).and_then(|mut output| {
-                let mut reader = BufReader::new(&bamfile);
-                bamrescue::rescue(&mut reader, &mut output, &logger)
-            })
-        }).unwrap_or_else(|cause| {
-            error!(logger, "Unable to rescue bam file: {}", cause);
-            process::exit(1);
-        });
     }
 }