From 3ed80f9e1664a5e411be655bb309620c6241a4aa Mon Sep 17 00:00:00 2001
From: snayfach <snayfach@gmail.com>
Date: Sat, 12 Nov 2016 13:28:34 -0800
Subject: [PATCH 1/2] Fixed bug when parsing mpileup

---
 midas/run/snps.py | 38 +++++++++++++++++++++-----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/midas/run/snps.py b/midas/run/snps.py
index 5076d48..9a631ea 100644
--- a/midas/run/snps.py
+++ b/midas/run/snps.py
@@ -138,29 +138,33 @@ def format_pileup(args, species, contigs):
 		#   write info from pileup
 		write_present(sp.out, pileup=p)
 		sp.j += 1
+
+		# end of contig
 		if sp.j >= contig.length:
 			sp.i += 1; sp.j = 0
-			contig = contigs[sp.contigs[sp.i]]
 
 	# fill in downstream positions & contigs with zero coverage
 	for sp in species.values():
 		
-		# lefover positions on last contig
-		#   indicates that one or more downstream positions have zero coverage
-		contig = contigs[sp.contigs[sp.i]]
-		while sp.j < contig.length:
-			write_missing(sp.out, ref_id=contig.id, ref_pos=str(sp.j+1), ref_allele=contig.seq[sp.j])
-			sp.j += 1
-
-		# lefover contigs
-		#   indicates that one or more downstream contigs have zero coverage
-		sp.i += 1; sp.j = 0
-		while sp.i < len(sp.contigs):
+		# no remaining contigs
+		if sp.i < len(sp.contigs):
+		
+			# lefover positions on last contig
+			#   indicates that one or more downstream positions have zero coverage
 			contig = contigs[sp.contigs[sp.i]]
-			write_missing(sp.out, ref_id=contig.id, ref_pos=str(sp.j+1), ref_allele=contig.seq[sp.j])
-			sp.j += 1
-			if sp.j >= contig.length:
-				sp.i += 1; sp.j = 0
+			while sp.j < contig.length:
+				write_missing(sp.out, ref_id=contig.id, ref_pos=str(sp.j+1), ref_allele=contig.seq[sp.j])
+				sp.j += 1
+
+			# lefover contigs
+			#   indicates that one or more downstream contigs have zero coverage
+			sp.i += 1; sp.j = 0
+			while sp.i < len(sp.contigs):
+				contig = contigs[sp.contigs[sp.i]]
+				write_missing(sp.out, ref_id=contig.id, ref_pos=str(sp.j+1), ref_allele=contig.seq[sp.j])
+				sp.j += 1
+				if sp.j >= contig.length:
+					sp.i += 1; sp.j = 0
 
 		# close output files
 		sp.out.close()
@@ -281,7 +285,7 @@ def run_pipeline(args):
 		start = time()
 		print("\nRunning mpileup")
 		args['log'].write("\nRunning mpileup\n")
-		pileup(args)
+#		pileup(args)
 		print("  %s minutes" % round((time() - start)/60, 2) )
 		print("  %s Gb maximum memory" % utility.max_mem_usage())
 

From bbd31095686cc2aee8b047b207024febee5623d4 Mon Sep 17 00:00:00 2001
From: snayfach <snayfach@gmail.com>
Date: Sat, 12 Nov 2016 13:32:15 -0800
Subject: [PATCH 2/2] Increment version number

---
 midas/utility.py | 2 +-
 setup.py         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/midas/utility.py b/midas/utility.py
index bcb38c5..a4c1496 100644
--- a/midas/utility.py
+++ b/midas/utility.py
@@ -6,7 +6,7 @@
 
 import io, os, stat, sys, resource, gzip, platform, subprocess, bz2
 
-__version__ = '1.2.0'
+__version__ = '1.2.1'
 
 def which(program):
 	""" Mimics unix 'which' function """
diff --git a/setup.py b/setup.py
index e208915..a7cf744 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
 	name = 'MIDAS',
-	version = '1.2.0',
+	version = '1.2.1',
 	description = 'An integrated pipeline and for estimating species and strain-level genomic variation from metagenomic data',
 	license = 'GPL',
 	author = 'Stephen Nayfach',