From d49092621ac1070d201c162a0a1d29dd59605311 Mon Sep 17 00:00:00 2001
From: NuttyLogic <colinpfarrell@gmail.com>
Date: Mon, 29 Mar 2021 18:14:15 -0700
Subject: [PATCH] Methylation Calling Max Depth Fix

---
 bsbolt/External/HTSLIB/config.log | 8 ++++----
 bsbolt/Utils/Launcher.py          | 1 +
 bsbolt/Utils/Parser.py            | 2 +-
 setup.py                          | 2 +-
 tests/test_alignment_pipeline.py  | 3 ++-
 5 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/bsbolt/External/HTSLIB/config.log b/bsbolt/External/HTSLIB/config.log
index 71fc8b2..11e35a4 100644
--- a/bsbolt/External/HTSLIB/config.log
+++ b/bsbolt/External/HTSLIB/config.log
@@ -266,7 +266,7 @@ configure:4398: $? = 0
 configure:4398: result: yes
 configure:4398: checking for srand48_deterministic
 configure:4398: gcc -o conftest  -Wall -g -O2 -fvisibility=hidden   -fvisibility=hidden conftest.c  >&5
-/usr/bin/ld: /tmp/ccKRiYWC.o: in function `main':
+/usr/bin/ld: /tmp/ccow2Qrt.o: in function `main':
 /home/colin/Documents/BSBoltDev/BSBolt/bsbolt/External/HTSLIB/conftest.c:61: undefined reference to `srand48_deterministic'
 collect2: error: ld returned 1 exit status
 configure:4398: $? = 1
@@ -351,7 +351,7 @@ conftest.c:35:6: warning: conflicting types for built-in function 'log'; expecte
       |      ^~~
 conftest.c:1:1: note: 'log' is declared in header '<math.h>'
     1 | /* confdefs.h */
-/usr/bin/ld: /tmp/ccyDK3LO.o: in function `main':
+/usr/bin/ld: /tmp/ccPtDqyE.o: in function `main':
 /home/colin/Documents/BSBoltDev/BSBolt/bsbolt/External/HTSLIB/conftest.c:39: undefined reference to `log'
 collect2: error: ld returned 1 exit status
 configure:4580: $? = 1
@@ -514,7 +514,7 @@ configure:5039: $? = 0
 configure:5048: result: yes
 configure:5179: checking for CCHmac
 configure:5179: gcc -o conftest  -Wall -g -O2 -fvisibility=hidden   -fvisibility=hidden conftest.c -lz -lm  >&5
-/usr/bin/ld: /tmp/cc0lfQFB.o: in function `main':
+/usr/bin/ld: /tmp/ccds9Frq.o: in function `main':
 /home/colin/Documents/BSBoltDev/BSBolt/bsbolt/External/HTSLIB/conftest.c:65: undefined reference to `CCHmac'
 collect2: error: ld returned 1 exit status
 configure:5179: $? = 1
@@ -590,7 +590,7 @@ configure: failed program was:
 configure:5179: result: no
 configure:5186: checking for library containing HMAC
 configure:5217: gcc -o conftest  -Wall -g -O2 -fvisibility=hidden   -fvisibility=hidden conftest.c -lz -lm  >&5
-/usr/bin/ld: /tmp/ccfRKnMI.o: in function `main':
+/usr/bin/ld: /tmp/cc9Tf9Ix.o: in function `main':
 /home/colin/Documents/BSBoltDev/BSBolt/bsbolt/External/HTSLIB/conftest.c:42: undefined reference to `HMAC'
 collect2: error: ld returned 1 exit status
 configure:5217: $? = 1
diff --git a/bsbolt/Utils/Launcher.py b/bsbolt/Utils/Launcher.py
index 8f9dcb5..d94a74e 100644
--- a/bsbolt/Utils/Launcher.py
+++ b/bsbolt/Utils/Launcher.py
@@ -129,6 +129,7 @@ def launch_methylation_call(arguments):
                                       min_read_depth=arguments.min,
                                       threads=arguments.t,
                                       verbose=arguments.verbose,
+                                      max_read_depth=arguments.max,
                                       min_base_quality=arguments.BQ,
                                       min_mapping_quality=arguments.MQ,
                                       cg_only=arguments.CG,
diff --git a/bsbolt/Utils/Parser.py b/bsbolt/Utils/Parser.py
index 6f39b09..4e3e4f4 100644
--- a/bsbolt/Utils/Parser.py
+++ b/bsbolt/Utils/Parser.py
@@ -3,7 +3,7 @@
 from bsbolt.Utils.ParserHelpMessages import aggregate_help, alignment_help, impute_help, index_help, meth_help, sim_help
 
 
-parser = argparse.ArgumentParser(description='BiSulfite Bolt v1.4.4',
+parser = argparse.ArgumentParser(description='BiSulfite Bolt v1.4.5',
                                  usage='bsbolt Module {Module Arguments}')
 
 subparsers = parser.add_subparsers(description='Please invoke bsbolt module for help,'
diff --git a/setup.py b/setup.py
index 2fb513a..1cafb9a 100644
--- a/setup.py
+++ b/setup.py
@@ -94,7 +94,7 @@ def run(self):
 
 
 setup(name='bsbolt',
-      version='1.4.4',
+      version='1.4.5',
       description='Bisulfite Sequencing Processing Platform',
       long_description=long_description,
       long_description_content_type="text/markdown",
diff --git a/tests/test_alignment_pipeline.py b/tests/test_alignment_pipeline.py
index 81e10b1..96af081 100644
--- a/tests/test_alignment_pipeline.py
+++ b/tests/test_alignment_pipeline.py
@@ -52,7 +52,8 @@
                             f'{bsb_directory}tests/BSB_pe_test.sorted.bam',
                             '-O', f'{bsb_directory}tests/BSB_pe_test',
                             '-DB', f'{bsb_directory}tests/TestData/BSB_Test_DB',
-                            '-t', '6', '-verbose', '-BQ', '10', '-MQ', '20', '-BG']
+                            '-t', '6', '-verbose', '-BQ', '10', '-MQ', '20', '-BG',
+                            '-max', '8000']
 subprocess.run(bs_call_methylation_args)
 
 # retrieve reference and test alignments