From 6fb1d2c6ebd000379a815ab8b20fc3955d69ffaf Mon Sep 17 00:00:00 2001
From: Andrea Telatin <andrea@telatin.com>
Date: Thu, 4 Mar 2021 18:16:47 +0000
Subject: [PATCH] v12

---
 bin/seqfu                  | Bin 1373352 -> 1373352 bytes
 seqfu.nimble               |   2 +-
 src/dadaist2_mergeseqs.nim |  47 ++++++++++++++++++++++++++++++-------
 3 files changed, 40 insertions(+), 9 deletions(-)

diff --git a/bin/seqfu b/bin/seqfu
index b30f5dc3a3e07ca09fd36f831f985c40c220ed19..c1b0034a269fa6d3f3088746050bd006354cd6ee 100755
GIT binary patch
delta 123
zcmZ4SGI+(y;0=42L;`#6v=>?4lDo*fQiP@WU{uWRwbPp~FtuM`VgzCk%?!jWK+Fon
zY(UHo#2i4(3B+7L%nigmK+Frod_c?(!~)wdFbSsKWi)CxdmsqJLO?9M-Ryx#kq7{2
CgD{)`

delta 123
zcmZ4SGI+(y;0=42L^jU;v$9YAn5g+gv!(@s`J2Q~t$NvffvNoh6C)6VXl5X00b*7l
zW&>h&Am#vKP9Ww2Vs0Sj0b*Vt<^y7WAQsqufk`m+E~8<)*#ki!76M}7?Pd=|ibMe2
ChcUST

diff --git a/seqfu.nimble b/seqfu.nimble
index 040aea6..df98af6 100644
--- a/seqfu.nimble
+++ b/seqfu.nimble
@@ -1,5 +1,5 @@
 # Package
-version       = "0.8.11"
+version       = "0.8.12"
 author        = "Andrea Telatin"
 description   = "SeqFU command-line tools"
 license       = "MIT"
diff --git a/src/dadaist2_mergeseqs.nim b/src/dadaist2_mergeseqs.nim
index 95dbd11..817ebb9 100644
--- a/src/dadaist2_mergeseqs.nim
+++ b/src/dadaist2_mergeseqs.nim
@@ -13,14 +13,42 @@ proc handler() {.noconv.} =
   raise newException(EKeyboardInterrupt, "Keyboard Interrupt")
 setControlCHook(handler)
 
-proc combine(x, y: string): string =
+proc compare(x, y: string, maxMismatches: int): bool =
+  if len(x) != len(y):
+    return false
+  var
+    mismatches = 0
+  
+  if x == y:
+    return true
+
   for i in 0 .. x.high:
-    let
-      xSlice =  x[i .. y.high]
-      ySlice =  y[0 .. min(xSlice.high, y.high)]
-    if xSlice == ySlice:
-      return x[0 ..< i] & y
-  return ""
+    if x[i] != y[i]:
+      mismatches += 1
+      if mismatches > maxMismatches:
+        return false
+  return true
+
+
+proc combine(x, y: string, maxMismatches: int): string =
+  if maxMismatches == 0:
+    for i in 0 .. x.high:
+      let
+        xSlice =  x[i .. y.high]
+        ySlice =  y[0 .. min(xSlice.high, y.high)]
+      if xSlice == ySlice:
+        return x[0 ..< i] & y
+    return ""
+  else:
+    for i in 0 .. x.high:
+      let
+        xSlice =  x[i .. y.high]
+        ySlice =  y[0 .. min(xSlice.high, y.high)]
+      if compare(xSlice, ySlice, maxMismatches):
+        echo ">", x[0 ..< i] & y
+        echo "<", x
+        return x[0 ..< i] & y
+    return ""
   
 proc main(): int =
   let args = docopt("""
@@ -35,6 +63,7 @@ proc main(): int =
     -p, --pair-spacer STRING   Pairs separator [default: NNNNNNNNNN]
     -s, --strip STRING         Remove this string from sample names
     -n, --seq-name STRING      Sequence string name [default: MD5]
+    -m, --max-mismatches INT   Maximum allowed mismatches [default: 0]
     --id STRING                Features column name [default: #OTU ID]
     --verbose                  Print verbose output
 
@@ -79,6 +108,8 @@ proc main(): int =
   # Output: header
   echo (p.headers).join("\t")
 
+  let
+    maxMismatches = parseInt($args["--max-mismatches"])
   var
     counter = 0
     joined = 0
@@ -93,7 +124,7 @@ proc main(): int =
       fragments = repSeq.split($args["--pair-spacer"])
 
     if fragments.high == 1:
-      merge = combine(fragments[0], fragments[1])
+      merge = combine(fragments[0], fragments[1], maxMismatches)
       split += 1
     elif args["--verbose"]:
       stderr.writeLine("Sequence not splittable at ", counter)