From 3dd461e252211a3aa336361651dbc079d36fb6c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Mokrej=C5=A1?= <mmokrejs@gmail.com>
Date: Thu, 25 Jan 2018 19:58:54 +0100
Subject: [PATCH 1/2] Support multiple input SAM/BAM files

Iterate over all input files while increasing internal counters
and after that print out the statistics.
---
 src/bin/sga-astat.py | 70 ++++++++++++++++++++++----------------------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/src/bin/sga-astat.py b/src/bin/sga-astat.py
index 819b6a2c..a0ef71f3 100755
--- a/src/bin/sga-astat.py
+++ b/src/bin/sga-astat.py
@@ -30,8 +30,8 @@ def computeAStat(arrivalRate, len, n):
 arrivalRate = 0
 
 def usage():
-    print 'usage: sga-astat.py in.bam'
-    print 'Compute Myers\' a-statistic for a set of contigs using the read alignments in in.bam'
+    print 'usage: sga-astat.py [OPTIONS] *.bam'
+    print 'Compute Myers\' a-statistic for a set of contigs using the read alignments from at least one SAM/BAM file'
     print 'Options:'
     print '    -m=INT          only compute a-stat for contigs at least INT bases in length'
     print '    -b=INT          use the longest INT contigs to perform the initial estimate'
@@ -62,53 +62,53 @@ def usage():
             usage()
             sys.exit(1)
 
-if len(args) == 0:
-    print 'Error: a BAM file must be provided\n'
+if not args:
+    print 'Error: at least one SAM/BAM file must be provided\n'
     usage()
     sys.exit(2)
 
-bamFilename = args[0]
-
-sys.stderr.write('Reading alignments from ' + bamFilename + '\n')
 contigData = list()
-
-# Read the contig names and lengths from the bam
-bamFile = pysam.Samfile(bamFilename, "rb")
-
-for (name, length) in zip(bamFile.references, bamFile.lengths):
-    t = name, length, 0
-    contigData.append(ContigData(name, length))
-    #print 'Name: ' + name
-    #print 'Length: ' + str(len)
-
-# Read the alignments and populate the counts
 totalReads = 0
 sumReadLength = 0
-
 last_ref_idx = -1
 last_pos = -1
 
-for alignment in bamFile:
+for bamFilename in args:
+    sys.stderr.write('Reading alignments from ' + bamFilename + '\n')
+
+    # Read the contig names and lengths from the bam
+    bamFile = pysam.Samfile(bamFilename, "rb")
+
+    for (name, length) in zip(bamFile.references, bamFile.lengths):
+        t = name, length, 0
+        contigData.append(ContigData(name, length))
+        #print 'Name: ' + name
+        #print 'Length: ' + str(len)
+
+    # Read the alignments and populate the counts
+    for alignment in bamFile:
+
+        if alignment.is_unmapped:
+            continue
 
-    if alignment.is_unmapped:
-        continue
+        ref_idx = alignment.rname
+        ref_name = bamFile.getrname(ref_idx)
 
-    ref_idx = alignment.rname
-    ref_name = bamFile.getrname(ref_idx)
+        pos = alignment.pos
 
-    pos = alignment.pos
+        if ref_idx == last_ref_idx and pos == last_pos and not bKeepDuplicates:
+            continue
 
-    if ref_idx == last_ref_idx and pos == last_pos and not bKeepDuplicates:
-        continue
+        # Update the count
+        cd = contigData[ref_idx]
+        cd.n += 1
+        totalReads += 1
+        sumReadLength += alignment.rlen
+        assert(cd.name == ref_name)
+        last_ref_idx = ref_idx
+        last_pos = pos
 
-    # Update the count
-    cd = contigData[ref_idx]
-    cd.n += 1
-    totalReads += 1
-    sumReadLength += alignment.rlen
-    assert(cd.name == ref_name)
-    last_ref_idx = ref_idx
-    last_pos = pos
+    bamFile.close()
 
 avgReadLen = sumReadLength / totalReads
 contigData.sort(key=lambda c : c.len, reverse=True)

From e6565dc3d3ca747a2f6e659f62d20235efb111a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Mokrej=C5=A1?= <mmokrejs@gmail.com>
Date: Thu, 25 Jan 2018 20:39:34 +0100
Subject: [PATCH 2/2] Fix typo in INVERSESUFFIXARRAH_H (issue #109)

---
 src/SuffixTools/InverseSuffixArray.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/SuffixTools/InverseSuffixArray.h b/src/SuffixTools/InverseSuffixArray.h
index 0d8c4ab2..dd3cc5e8 100644
--- a/src/SuffixTools/InverseSuffixArray.h
+++ b/src/SuffixTools/InverseSuffixArray.h
@@ -8,7 +8,7 @@
 // Implemented as a Vector of Vectors
 //
 #ifndef INVERSESUFFIXARRAY_H
-#define INVERSESUFFIXARRAH_H
+#define INVERSESUFFIXARRAY_H
 #include "STCommon.h"
 #include "SuffixArray.h"