{"action":"closed","issue":{"url":"https://api.github.com/repos/etal/cnvkit/issues/336","repository_url":"https://api.github.com/repos/etal/cnvkit","labels_url":"https://api.github.com/repos/etal/cnvkit/issues/336/labels{/name}","comments_url":"https://api.github.com/repos/etal/cnvkit/issues/336/comments","events_url":"https://api.github.com/repos/etal/cnvkit/issues/336/events","html_url":"https://github.com/etal/cnvkit/issues/336","id":305757355,"node_id":"MDU6SXNzdWUzMDU3NTczNTU=","number":336,"title":"a option to count multiple alignment reads once only for 'cnvkit.py coverage'?","user":{"login":"wangyugui","id":13562993,"node_id":"MDQ6VXNlcjEzNTYyOTkz","avatar_url":"https://avatars2.githubusercontent.com/u/13562993?v=4","gravatar_id":"","url":"https://api.github.com/users/wangyugui","html_url":"https://github.com/wangyugui","followers_url":"https://api.github.com/users/wangyugui/followers","following_url":"https://api.github.com/users/wangyugui/following{/other_user}","gists_url":"https://api.github.com/users/wangyugui/gists{/gist_id}","starred_url":"https://api.github.com/users/wangyugui/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wangyugui/subscriptions","organizations_url":"https://api.github.com/users/wangyugui/orgs","repos_url":"https://api.github.com/users/wangyugui/repos","events_url":"https://api.github.com/users/wangyugui/events{/privacy}","received_events_url":"https://api.github.com/users/wangyugui/received_events","type":"User","site_admin":false},"labels":[{"id":112211064,"node_id":"MDU6TGFiZWwxMTIyMTEwNjQ=","url":"https://api.github.com/repos/etal/cnvkit/labels/question","name":"question","color":"cc317c","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-03-15T23:47:48Z","updated_at":"2018-08-13T02:15:10Z","closed_at":"2018-08-13T02:15:10Z","author_association":"NONE","body":"Hi.\r\n\r\nNeed we add a option to count multiple alignment reads once only for 'cnvkit.py coverage'?\r\njust like 'samtools view -F 0x900'\r\n\r\nall of multiple alignment reads  have MAPQ 0; but only one is the primary, and others have a 0x100 flags.\r\n\r\nThis is part of a WGS NA12787 result. It seems that the depth  is not stable enough.\r\n\r\n```\r\nchromosome      start   end     gene    depth   log2\r\n1       10000   207666  -       61.9088 5.95207\r\n1       257666  297968  -       100.642 6.65309\r\n1       347968  535988  -       51.2135 5.67845\r\n1       585988  2648795 -       72.2569 6.17506\r\n1       2663389 2666954 -       1038.97 10.0209\r\nchromosome      start   end     gene    depth   log2\r\n1       10000   207666  -       61.9088 5.95207\r\n1       257666  297968  -       100.642 6.65309\r\n1       347968  535988  -       51.2135 5.67845\r\n1       585988  2648795 -       72.2569 6.17506\r\n1       2663389 2666954 -       1038.97 10.0209\r\n1       2702586 2702781 -       2320.57 11.1803\r\n1       2746290 2746520 -       1910.4  10.8997\r\n1       2777253 12954384        -       63.9831 5.99962\r\n1       13004384        16799163        -       69.9015 6.12725\r\n1       16849163        121976459       -       65.0335 6.02311\r\n1       122026459       122027289       -       41.2277 5.36554\r\n1       124932223       124999065       -       139.209 7.12111\r\n1       125007407       125021705       -       65.6206 6.03608\r\n1       125062824       125184587       -       618.727 9.27316\r\n1       143184587       223558935       -       66.5986 6.05742\r\n1       223608935       223609152       -       56.9631 5.83196\r\n1       223665734       228558364       -       65.2233 6.02732\r\n1       228608364       248946422       -       63.674  5.99263\r\n2       10000   1522913 -       60.4802 5.91839\r\n2       1538001 87405896        -       64.1983 6.00446\r\n2       87426437        89330679        -       64.9949 6.02225\r\n2       89530679        89685992        -       114.81  6.8431\r\n2       89753992        90402511        -       152.083 7.24871\r\n2       91402511        91504018        -       155.272 7.27865\r\n2       91513896        91515886        -       83.7739 6.38843\r\n2       91522299        92085424        -       83.0273 6.37551\r\n2       92137653        92138145        -       3284.17 11.6813\r\n2       92188145        92188971        -       5579.38 12.4459\r\n2       94090068        94090557        -       7061.64 12.7858\r\n2       94140557        94293015        -       625.817 9.2896\r\n2       94496015        94499652        -       69.1993 6.11269\r\n2       94569708        97439618        -       68.3523 6.09492\r\n2       91402511        91504018        -       155.272 7.27865\r\n2       91513896        91515886        -       83.7739 6.38843\r\n2       91522299        92085424        -       83.0273 6.37551\r\n2       92137653        92138145        -       3284.17 11.6813\r\n2       92188145        92188971        -       5579.38 12.4459\r\n2       94090068        94090557        -       7061.64 12.7858\r\n2       94140557        94293015        -       625.817 9.2896\r\n2       94496015        94499652        -       69.1993 6.11269\r\n2       94569708        97439618        -       68.3523 6.09492\r\n2       97489618        132209312       -       62.8329 5.97345\r\n2       132219958       132223356       -       99.5088 6.63675\r\n2       132230998       132238877       -       93.1814 6.54197\r\n2       132247099       231823752       -       63.8173 5.99588\r\n2       231846073       242183529       -       63.9627 5.99916\r\n3       10000   90299974        -       63.348  5.98523\r\n3       90306571        90323558        -       66.9403 6.0648\r\n3       90333755        90340630        -       61.7654 5.94873\r\n3       90356277        90357090        -       70.4071 6.13765\r\n3       90369052        90388949        -       44.163  5.46477\r\n3       90418749        90422027        -       67.971  6.08685\r\n3       90430336        90722458        -       99.4988 6.63661\r\n3       90772458        91249905        -       71.8412 6.16674\r\n3       91256421        91265381        -       29.9473 4.90436\r\n3       91276994        91519539        -       60.2025 5.91175\r\n3       91536338        91554254        -       1951.26 10.9302\r\n3       93655054        93655574        -       2016.36 10.9775\r\n3       93705574        93773507        -       479.344 8.90492\r\n3       93799784        195478537       -       63.7464 5.99427\r\n3       195506878       197384253       -       68.6957 6.10215\r\n```\r\n\r\nBest Regards\r\n"}}
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