Add -m as short option for scaffold filter

Now can use -n and -m together for cleaner syntax:
  -n 1:1 -m 1:1  (aggressive filtering)
  -n many -m 1:1 (default)
  -n 1 -m 1      (1:many on both)

Updated documentation to reflect this change.

Author: ekg

CLAUDE.md

@@ -87,7 +87,7 @@ The filtering process follows this exact sequence:
 4. **Scaffold Filter** (default: 1:1)
    - Apply plane sweep filtering to the SCAFFOLD chains
    - Respects PanSN prefix grouping when `-Y` is set
-   - Controlled by `--scaffold-filter` (default: "1:1")
+   - Controlled by `-m/--scaffold-filter` (default: "1:1")
    - Options: "1:1", "1" (same as "1:∞"), "N" (no filtering)
    - Keeps best scaffolds per query/target pair within each prefix group
 
@@ -101,7 +101,7 @@ The filtering process follows this exact sequence:
 ## Key Parameters
 
 - `-n/--num-mappings`: Primary mapping filter before scaffolds (default: "many" = no filtering)
-- `--scaffold-filter`: Filter for scaffold chains (default: "1:1")
+- `-m/--scaffold-filter`: Filter for scaffold chains (default: "1:1")
 - `-s/--scaffold-mass`: Minimum scaffold length (default: 10kb)
 - `-j/--scaffold-jump`: Maximum gap to merge mappings into scaffolds (default: 10kb)
 - `-d/--scaffold-dist`: Maximum distance for rescue (default: 20kb)
@@ -148,12 +148,12 @@ This would make the pipeline stages explicit and composable, reducing confusion
 
 1. **Default (wfmash-like)**: No pre-filtering, 1:1 scaffold filtering
    ```
-   sweepga -S 10000  # Creates scaffolds, keeps best per genome pair
+   sweepga  # Creates scaffolds, keeps best per chromosome pair
    ```
 
 2. **Aggressive filtering**: 1:1 pre-filtering, 1:1 scaffold filtering
    ```
-   sweepga -S 10000 -n 1:1 --scaffold-filter 1:1
+   sweepga -n 1:1 -m 1:1
    ```
 
 3. **Pre-filter only**: No scaffolding
@@ -163,7 +163,7 @@ This would make the pipeline stages explicit and composable, reducing confusion
 
 4. **Keep more mappings**: 1:∞ for both filters
    ```
-   sweepga -S 10000 -n 1 --scaffold-filter 1   # "1" is shorthand for "1:∞"
+   sweepga -n 1 -m 1   # "1" is shorthand for "1:∞"
    ```
 
 ## Key Differences from Original Description

README.md

@@ -70,7 +70,7 @@ grep -c "st:Z:rescued" data/scerevisiae8.filtered.paf   # Rescued mappings
 - **No pre-filtering** (`-n many`): All mappings participate in scaffold building
 - **Scaffold creation** (`-j 10k`): Merge mappings within 10kb gaps
 - **Min scaffold** (`-s 10k`): Scaffolds must be ≥10kb
-- **1:1 scaffold filter** (`--scaffold-filter 1:1`): Keep best scaffold per chromosome pair
+- **1:1 scaffold filter** (`-m 1:1`): Keep best scaffold per chromosome pair
 - **Rescue distance** (`-d 20k`): Rescue mappings within 20kb of scaffolds
 
 ## Parameters
@@ -91,7 +91,7 @@ grep -c "st:Z:rescued" data/scerevisiae8.filtered.paf   # Rescued mappings
 
 `-d/--scaffold-dist` sets the maximum Euclidean distance for rescue (default 20k). Mappings further than this from any scaffold anchor are discarded.
 
-`--scaffold-filter` controls scaffold filtering (default "1:1"). Options: "1:1", "1" (1:many), "many" (no filter).
+`-m/--scaffold-filter` controls scaffold filtering (default "1:1"). Options: "1:1", "1" (1:many), "many" (no filter).
 
 ### Chain Annotations
 

src/main.rs

@@ -96,7 +96,7 @@ struct Args {
     num_mappings: String,
 
     /// Scaffold filter: "1:1" (best), "M:N" (top M per query, N per target; ∞/many for unbounded)
-    #[clap(long = "scaffold-filter", default_value = "1:1")]
+    #[clap(short = 'm', long = "scaffold-filter", default_value = "1:1")]
     scaffold_filter: String,
 
     /// Scaffold jump (gap) distance. 0 = disable scaffolding (plane sweep only), >0 = enable scaffolding