Merge branch 'develop' into feature-extract_aligned_fastq

.gitignore

.idea/.name

.idea/compiler.xml

.idea/copyright/profiles_settings.xml

.idea/dictionaries/warindrarto.xml

.idea/encodings.xml

.idea/inspectionProfiles/Project_Default.xml

.idea/inspectionProfiles/profiles_settings.xml

.idea/libraries/Maven__com_baqend_bloom_filter_1_02.xml

.idea/libraries/Maven__com_beust_jcommander_1_27.xml

...n__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml

.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml

.idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml

.idea/libraries/Maven__com_google_guava_guava_17_0.xml

.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml

.idea/libraries/Maven__junit_junit_4_10.xml

...libraries/Maven__org_apache_commons_commons_pool2_2_2.xml

.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml

.idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml

...ibraries/Maven__org_biojava_biojava3_sequencing_3_1_0.xml