From 71320f99c5751c7c589fea9982079842b969db13 Mon Sep 17 00:00:00 2001
From: Jillian Rowe <jillian.e.rowe@gmail.com>
Date: Mon, 15 Feb 2016 10:42:19 +0400
Subject: [PATCH] commiting fixes for pull request

---
 bin/.python-version |   1 +
 bin/build_bithash   |   2 +-
 bin/correct         |   2 +-
 bin/count-kmers     |   2 +-
 bin/count-qmers     |   2 +-
 bin/cov_model.pyc   | Bin 0 -> 6561 bytes
 bin/quake.py        |  36 ++++++++++++++++++------------------
 bin/quake.pyc       | Bin 0 -> 10372 bytes
 8 files changed, 23 insertions(+), 22 deletions(-)
 create mode 100644 bin/.python-version
 create mode 100644 bin/cov_model.pyc
 create mode 100644 bin/quake.pyc

diff --git a/bin/.python-version b/bin/.python-version
new file mode 100644
index 0000000..7dceab0
--- /dev/null
+++ b/bin/.python-version
@@ -0,0 +1 @@
+2.7.10
diff --git a/bin/build_bithash b/bin/build_bithash
index b0ec855..cc8197a 120000
--- a/bin/build_bithash
+++ b/bin/build_bithash
@@ -1 +1 @@
-../src/build_bithash
\ No newline at end of file
+../src/build_bithash.cpp
\ No newline at end of file
diff --git a/bin/correct b/bin/correct
index 054125a..1d413de 120000
--- a/bin/correct
+++ b/bin/correct
@@ -1 +1 @@
-../src/correct
\ No newline at end of file
+../src/correct.cpp
\ No newline at end of file
diff --git a/bin/count-kmers b/bin/count-kmers
index 5cf1171..58d9b50 120000
--- a/bin/count-kmers
+++ b/bin/count-kmers
@@ -1 +1 @@
-../src/count-kmers
\ No newline at end of file
+../src/count-kmers.cpp
\ No newline at end of file
diff --git a/bin/count-qmers b/bin/count-qmers
index 810dc93..580c8ac 120000
--- a/bin/count-qmers
+++ b/bin/count-qmers
@@ -1 +1 @@
-../src/count-qmers
\ No newline at end of file
+../src/count-qmers.cpp
\ No newline at end of file
diff --git a/bin/cov_model.pyc b/bin/cov_model.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..4240aaf878fe6f8c312313f844d6954dac48bff3
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diff --git a/bin/quake.py b/bin/quake.py
index 190cb69..bee5c22 100755
--- a/bin/quake.py
+++ b/bin/quake.py
@@ -31,7 +31,7 @@ def main():
     # Count options
     count_group = OptionGroup(parser, 'K-mer counting')
     count_group.add_option('--no_jelly', dest='no_jelly', action='store_true', default=False, help='Count k-mers using a simpler program than Jellyfish')
-    count_group.add_option('--no_count', dest='no_count', action='store_true', default=False, help='Kmers are already counted and in expected file [reads file].qcts or [reads file].cts [default: %default]')    
+    count_group.add_option('--no_count', dest='no_count', action='store_true', default=False, help='Kmers are already counted and in expected file [reads file].qcts or [reads file].cts [default: %default]')
     count_group.add_option('--int', dest='count_kmers', action='store_true', default=False, help='Count kmers as integers w/o the use of quality values [default: %default]')
     count_group.add_option('--count_only', dest='count_only', action='store_true', default=False, help=SUPPRESS_HELP)
     count_group.add_option('--hash_size', dest='hash_size', type='int', help='Jellyfish hash-size parameter. Quake will estimate using k if not given')
@@ -115,16 +115,16 @@ def main():
     # correct reads
     ############################################
     correct_options = make_cor_opts(options)
-    if options.model_gc:        
+    if options.model_gc:
         # run correct C++ code
-        p = subprocess.Popen('%s/correct %s %s -m %s -a cutoffs.gc.txt -q %d' % (quake_dir, correct_options, reads_str, ctsf, quality_scale), shell=True)
+        p = subprocess.Popen('correct %s %s -m %s -a cutoffs.gc.txt -q %d' % ( correct_options, reads_str, ctsf, quality_scale), shell=True)
         os.waitpid(p.pid, 0)
 
     else:
-        cutoff = get_cutoff()            
+        cutoff = get_cutoff()
 
         # run correct C++ code
-        p = subprocess.Popen('%s/correct %s %s -m %s -c %s -q %d' % (quake_dir, correct_options, reads_str, ctsf, cutoff, quality_scale), shell=True)
+        p = subprocess.Popen('correct %s %s -m %s -c %s -q %d' % (correct_options, reads_str, ctsf, cutoff, quality_scale), shell=True)
         os.waitpid(p.pid, 0)
 
 
@@ -150,16 +150,16 @@ def count_kmers(readsf, reads_listf, k, ctsf, quality_scale):
     # none zipped
     if sum(fq_zipped) == 0:
         if ctsf[-5:] == '.qcts':
-            p = subprocess.Popen('cat %s | %s/count-qmers -k %d -q %d > %s' % (' '.join(fq_files), quake_dir, k, quality_scale, ctsf), shell=True)
+            p = subprocess.Popen('cat %s | count-qmers -k %d -q %d > %s' % (' '.join(fq_files), k, quality_scale, ctsf), shell=True)
         else:
-            p = subprocess.Popen('cat %s | %s/count-kmers -k %d > %s' % (' '.join(fq_files), quake_dir, k, ctsf), shell=True)
+            p = subprocess.Popen('cat %s | count-kmers -k %d > %s' % (' '.join(fq_files), k, ctsf), shell=True)
 
     # all zipped
     elif sum(fq_zipped) == len(fq_zipped):
         if ctsf[-5:] == '.qcts':
-            p = subprocess.Popen('gunzip -c %s | %s/count-qmers -k %d -q %d > %s' % (' '.join(fq_files), quake_dir, k, quality_scale, ctsf), shell=True)
+            p = subprocess.Popen('gunzip -c %s | count-qmers -k %d -q %d > %s' % (' '.join(fq_files), k, quality_scale, ctsf), shell=True)
         else:
-            p = subprocess.Popen('gunzip -c %s | %s/count-kmers -k %d > %s' % (' '.join(fq_files), quake_dir, k, ctsf), shell=True)
+            p = subprocess.Popen('gunzip -c %s | count-kmers -k %d > %s' % (' '.join(fq_files),  k, ctsf), shell=True)
 
     # mixed- boo
     else:
@@ -253,16 +253,16 @@ def jellyfish(readsf, reads_listf, k, ctsf, quality_scale, hash_size, proc):
     # none zipped
     if sum(fq_zipped) == 0:
         if ctsf[-4:] == 'qcts':
-            p = subprocess.Popen('%s/jellyfish count -q --quality-start %d -c %d -o %s.db -m %d -t %d -s %d --both-strands %s' % (jellyfish_dir, quality_scale, ct_size, output_pre, k, proc, hash_size, ' '.join(fq_files)), shell=True)
+            p = subprocess.Popen('jellyfish count -q --quality-start %d -c %d -o %s.db -m %d -t %d -s %d --both-strands %s' % (quality_scale, ct_size, output_pre, k, proc, hash_size, ' '.join(fq_files)), shell=True)
         else:
-            p = subprocess.Popen('%s/jellyfish count -c %d -o %s.db -m %d -t %d -s %d --both-strands %s' % (jellyfish_dir, ct_size, output_pre, k, proc, hash_size, ' '.join(fq_files)), shell=True)
+            p = subprocess.Popen('jellyfish count -c %d -o %s.db -m %d -t %d -s %d --both-strands %s' % ( ct_size, output_pre, k, proc, hash_size, ' '.join(fq_files)), shell=True)
 
     # all zipped
     elif sum(fq_zipped) == len(fq_zipped):
         if ctsf[-4:] == 'qcts':
-            p = subprocess.Popen('gunzip -c %s | %s/jellyfish count -q --quality-start %d -c %d -o %s.db -m %d -t %d -s %d --both-strands /dev/fd/0' % (' '.join(fq_files), jellyfish_dir, quality_scale, ct_size, output_pre, k, proc, hash_size), shell=True)
+            p = subprocess.Popen('gunzip -c %s | jellyfish count -q --quality-start %d -c %d -o %s.db -m %d -t %d -s %d --both-strands /dev/fd/0' % (' '.join(fq_files), quality_scale, ct_size, output_pre, k, proc, hash_size), shell=True)
         else:
-            p = subprocess.Popen('gunzip -c %s | %s/jellyfish count -c %d -o %s.db -m %d -t %d -s %d --both-strands /dev/fd/0' % (' '.join(fq_files), jellyfish_dir, ct_size, output_pre, k, proc, hash_size), shell=True)
+            p = subprocess.Popen('gunzip -c %s | jellyfish count -c %d -o %s.db -m %d -t %d -s %d --both-strands /dev/fd/0' % (' '.join(fq_files), ct_size, output_pre, k, proc, hash_size), shell=True)
 
     # mixed- boo
     else:
@@ -283,22 +283,22 @@ def jellyfish(readsf, reads_listf, k, ctsf, quality_scale, hash_size, proc):
             hash_size *= max_db
 
             # merge db
-            p = subprocess.Popen('%s/jellyfish qmerge -s %d -m %d -o %s.dbm %s' % (jellyfish_dir, hash_size, k, output_pre, ' '.join(['%s.db_%d' % (output_pre,i) for i in range(max_db)])), shell=True)
+            p = subprocess.Popen('jellyfish qmerge -s %d -m %d -o %s.dbm %s' % (hash_size, k, output_pre, ' '.join(['%s.db_%d' % (output_pre,i) for i in range(max_db)])), shell=True)
             os.waitpid(p.pid, 0)
-            
+
             # rename file
             os.rename('%s.dbm_0' % output_pre, '%s.dbm' % output_pre)
 
         else:
             # merge db
-            p = subprocess.Popen('%s/jellyfish merge -o %s.dbm %s' % (jellyfish_dir, output_pre, ' '.join(['%s.db_%d' % (output_pre,i) for i in range(max_db)])), shell=True)
+            p = subprocess.Popen('jellyfish merge -o %s.dbm %s' % (output_pre, ' '.join(['%s.db_%d' % (output_pre,i) for i in range(max_db)])), shell=True)
             os.waitpid(p.pid, 0)
 
     # produce actual counts
     if ctsf[-4:] == 'qcts':
-        p = subprocess.Popen('%s/jellyfish qdump -c %s.dbm > %s' % (jellyfish_dir, output_pre, ctsf), shell=True)
+        p = subprocess.Popen('jellyfish qdump -c %s.dbm > %s' % ( output_pre, ctsf), shell=True)
     else:
-        p = subprocess.Popen('%s/jellyfish dump -c %s.dbm > %s' % (jellyfish_dir, output_pre, ctsf), shell=True)
+        p = subprocess.Popen('jellyfish dump -c %s.dbm > %s' % ( output_pre, ctsf), shell=True)
     os.waitpid(p.pid, 0)
 
 
diff --git a/bin/quake.pyc b/bin/quake.pyc
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