Merge pull request #33 from google/r0.3.1

R0.3.1

Author: danielecook

README.md

@@ -75,15 +75,15 @@ to inspect some example model inputs and outputs.
 If you're on a GPU machine:
 
 ```bash
-pip install deepconsensus[gpu]==0.3.0
+pip install deepconsensus[gpu]==0.3.1
 # To make sure the `deepconsensus` CLI works, set the PATH:
 export PATH="/home/${USER}/.local/bin:${PATH}"
 ```
 
 If you're on a CPU machine:
 
 ```bash
-pip install deepconsensus[cpu]==0.3.0
+pip install deepconsensus[cpu]==0.3.1
 # To make sure the `deepconsensus` CLI works, set the PATH:
 export PATH="/home/${USER}/.local/bin:${PATH}"
 ```
@@ -93,13 +93,13 @@ export PATH="/home/${USER}/.local/bin:${PATH}"
 For GPU:
 
 ```bash
-sudo docker pull google/deepconsensus:0.3.0-gpu
+sudo docker pull google/deepconsensus:0.3.1-gpu
 ```
 
 For CPU:
 
 ```bash
-sudo docker pull google/deepconsensus:0.3.0
+sudo docker pull google/deepconsensus:0.3.1
 ```
 
 ### From source

README_pip.md

@@ -3,15 +3,15 @@
 If you're on a GPU machine:
 
 ```bash
-pip install deepconsensus[gpu]==0.3.0
+pip install deepconsensus[gpu]==0.3.1
 # To make sure the `deepconsensus` CLI works, set the PATH:
 export PATH="/home/${USER}/.local/bin:${PATH}"
 ```
 
 If you're on a CPU machine:
 
 ```bash
-pip install deepconsensus[cpu]==0.3.0
+pip install deepconsensus[cpu]==0.3.1
 # To make sure the `deepconsensus` CLI works, set the PATH:
 export PATH="/home/${USER}/.local/bin:${PATH}"
 ```

deepconsensus/inference/quick_inference.py

@@ -103,7 +103,7 @@ class DebugStage(enum.Enum):
 
 # The following parameters are used at the end for filtering the final output.
 flags.DEFINE_integer('min_length', 0, 'Minimum length for reads output.')
-flags.DEFINE_integer('min_quality', 0, 'Minimum quality for reads output.')
+flags.DEFINE_integer('min_quality', 20, 'Minimum quality for reads output.')
 
 # The following parameters affect performance of this script.
 flags.DEFINE_integer(

deepconsensus/utils/dc_constants.py

@@ -33,7 +33,7 @@
 import tensorflow as tf
 
 # DeepConsensus Version
-__version__ = '0.3.0'
+__version__ = '0.3.1'
 
 # Vocab
 GAP_OR_PAD = ' '

docs/quick_start.md

@@ -133,8 +133,8 @@ the appropriate version (CPU / GPU) depending on your use case.
 
 ```bash
 # Define DOCKER_IMAGE *once* depending on whether you will be using CPU or GPU:
-DOCKER_IMAGE=google/deepconsensus:0.3.0  # For CPU
-DOCKER_IMAGE=google/deepconsensus:0.3.0-gpu  # For GPU
+DOCKER_IMAGE=google/deepconsensus:0.3.1  # For CPU
+DOCKER_IMAGE=google/deepconsensus:0.3.1-gpu  # For GPU
 sudo docker pull ${DOCKER_IMAGE}
 ```
 
@@ -304,7 +304,7 @@ At the end of your run, you should see:
 
 ```
 Processed 178 ZMWs in 334.629 seconds
-Outcome counts: OutcomeCounter(empty_sequence=0, only_gaps_and_padding=0, failed_quality_filter=0, failed_length_filter=0, success=178)
+Outcome counts: OutcomeCounter(empty_sequence=0, only_gaps_and_padding=0, failed_quality_filter=3, failed_length_filter=0, success=175)
 ```
 
 ## Optimizing Runtime

notebooks/Inspecting_DeepConsensus_examples_and_running_model.ipynb

@@ -81,7 +81,7 @@
         }
       ],
       "source": [
-        "! pip install -qq deepconsensus[cpu]==0.3.0"
+        "! pip install -qq deepconsensus[cpu]==0.3.1"
       ]
     },
     {