From de0be7467c6f01c426364b64a8bd552b62ab9842 Mon Sep 17 00:00:00 2001
From: Rob Patro <rob@newton>
Date: Tue, 11 Oct 2022 10:53:14 -0400
Subject: [PATCH 1/2] add necessary value parsers for force-cells and
 expect-cells

---
 Cargo.lock  | 4 ++--
 src/main.rs | 6 ++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 006afc3..bcda213 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -82,9 +82,9 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.58"
+version = "1.0.65"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bb07d2053ccdbe10e2af2995a2f116c1330396493dc1269f6a91d0ae82e19704"
+checksum = "98161a4e3e2184da77bb14f02184cdd111e83bbbcc9979dfee3c44b9a85f5602"
 
 [[package]]
 name = "approx"
diff --git a/src/main.rs b/src/main.rs
index 0783c77..354d7a2 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -91,8 +91,10 @@ fn main() -> anyhow::Result<()> {
             -k --"knee-distance"  "attempt to determine the number of barcodes to keep using the knee distance method."
             )
         )
-        .arg(arg!(-e --"expect-cells" <EXPECTCELLS> "defines the expected number of cells to use in determining the (read, not UMI) based cutoff"))
-        .arg(arg!(-f --"force-cells" <FORCECELLS>  "select the top-k most-frequent barcodes, based on read count, as valid (true)"))
+        .arg(arg!(-e --"expect-cells" <EXPECTCELLS> "defines the expected number of cells to use in determining the (read, not UMI) based cutoff")
+             .value_parser(value_parser!(usize)))
+        .arg(arg!(-f --"force-cells" <FORCECELLS>  "select the top-k most-frequent barcodes, based on read count, as valid (true)")
+             .value_parser(value_parser!(usize)))
         .arg(
             arg!(-b --"valid-bc" <VALIDBC> "uses true barcode collected from a provided file")
             .value_parser(pathbuf_file_exists_validator)

From aa0f4abb388e464491652fb2e1b682e33b1df05c Mon Sep 17 00:00:00 2001
From: Rob Patro <rob@newton>
Date: Tue, 11 Oct 2022 12:26:41 -0400
Subject: [PATCH 2/2] fix!: fix parsing of force-cells and expect-cells

---
 Cargo.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Cargo.toml b/Cargo.toml
index 6db1418..494a087 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "alevin-fry"
-version = "0.7.0"
+version = "0.7.1"
 authors = [
   "Avi Srivastava <avi.srivastava@nyu.edu>",
   "Hirak Sarkar <hirak_sarkar@hms.harvard.edu>",