samtools/htsjdk

1.4.1 CRAM_lossless_roundtrip SAMRecordDuplicateComparator_make_methods_accessible ab_tabix_index_on_bgzip ak_asyncTribbleCloseThreads ak_makeTribbleReadingSynchronous ak_revup_dependencies bcmaster bt_sam_record_filters compression-level cram_ambiguity_bases_fix cram_compression_improvements cram_multiref_roundtrip_fixes dr_fix_travis_exit_status eb_breakout_extensions fix_file_extension_checks_in_makeSAMOrBAMwriter_and_makeWriter gg_RemoveInvalidCharacterFromComment gh-pages jc_buffered_writing lb_asynch_iterator_for_yossi lb_cleanup_sorting_code lb_move_SimpleInterval_methods_to_locatable lb_remove_release_picard_script lb_switch_to_codecov master nh_cache_representative_in_duplicate_set nh_dangling_cram_test nh_flag_fields_format_now_with_tests nh_pub_reg2bin nh_vcf_double revert-473-ak_jacoco revert-631-ak_histogram rhl_gt_has_any_attribute_920 rhl_handle_stdin rhl_liftover_max_overlap_924 rhl_tabix_read_bad_coord_908 tf_cleanup_read_beans tf_samrecord_better_flag_methods tf_sort_query_hash tf_upgrade_snappy tf_validate_read_length_vs_insert_size tf_vcb_attributes vrr_vc_attr_as_list vrr_vcf_query_locatable yf_add_tests yf_add_unknown_SO yf_fix_NPE_in_md5OutputStream yf_intel_unittest yf_make_codecov_less_sensitive yf_make_get_header_possible_from_cram_with_no_reference yf_make_star_allele_symbolic

bc_4.13 2.10.1 2.10.0 2.9.1 2.9.0 2.8.1 2.8.0 2.7.0 2.6.1 2.6.0 2.5.1 2.5.0 2.4.1 2.4.0 2.3.0 2.3.0_buildhotfix 2.2.4 2.2.3 2.2.2 2.2.1 2.2.0 2.1.1 2.1.0 2.0.1 2.0.0 1.142 1.141 1.140 1.139 1.138 1.137 1.136 1.135 1.134 1.133 1.131 1.130 1.129 1.128 1.127 1.126 1.125 1.124 1.123 1.122 1.121 1.120 1.119 1.118 1.117 1.116 1.115 1.114 1.113