{"action":"opened","issue":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/71","labels_url":"https://api.github.com/repos/marcelm/cutadapt/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/marcelm/cutadapt/issues/71/comments","events_url":"https://api.github.com/repos/marcelm/cutadapt/issues/71/events","html_url":"https://github.com/marcelm/cutadapt/issues/71","id":61275700,"number":71,"title":"Change between 1.0 and 1.2.1: Ungreedy adapter cutting","user":{"login":"marcelm","id":724864,"avatar_url":"https://avatars.githubusercontent.com/u/724864?v=3","gravatar_id":"","url":"https://api.github.com/users/marcelm","html_url":"https://github.com/marcelm","followers_url":"https://api.github.com/users/marcelm/followers","following_url":"https://api.github.com/users/marcelm/following{/other_user}","gists_url":"https://api.github.com/users/marcelm/gists{/gist_id}","starred_url":"https://api.github.com/users/marcelm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marcelm/subscriptions","organizations_url":"https://api.github.com/users/marcelm/orgs","repos_url":"https://api.github.com/users/marcelm/repos","events_url":"https://api.github.com/users/marcelm/events{/privacy}","received_events_url":"https://api.github.com/users/marcelm/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/marcelm/cutadapt/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/marcelm/cutadapt/labels/imported","name":"imported","color":"FFFFFF"},{"url":"https://api.github.com/repos/marcelm/cutadapt/labels/wontfix","name":"wontfix","color":"ffffff"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-03-13T22:22:00Z","updated_at":"2015-03-13T22:22:00Z","closed_at":null,"body":"_From [ericfour...@gmail.com](https://code.google.com/u/102412943175425229035/) on May 03, 2013 17:07:26_\n\nThere is a \"breaking\" change in behaviour between version 1.0 and 1.2.1.\r\n\r\nI have a multiplexed paired-end sequencing library with a lot of read-through. This causes the reverse complement of the 4-base multiplexing adapter to be found at the 3' end of my reads. Version 1.0 of cutadapt cut the last 4 bases, and the last 4 bases only, whereas version 1.2.1 trims anything beyond the first instance of the 4-mer, regardless of its position.\r\n\r\nIn my case, the behaviour from 1.0 is the correct one, and I haven't found any way to obtain it using version 1.2.1. I've reverted back to using version 1.0, but it would be nice to have an \"ungreedy\" option.\r\n\r\nI've included the output from both versions below.\r\n\r\nUsing version 1.0, I get the following:\r\n\r\ncutadapt version 1.0\r\nCommand line parameters: -f fastq -a TGAC -o temp_R2.fastq Output/Libraries/1c/a. R2 .fastq\r\nMaximum error rate: 10.00&#37;\r\n   Processed reads: 22408330\r\n     Trimmed reads: 15739419 ( 70.2&#37;)\r\n   Too short reads: 0 (  0.0&#37; of processed reads)\r\n    Too long reads: 0 (  0.0&#37; of processed reads)\r\n        Total time:    833.72 s\r\n     Time per read:      0.04 ms\r\n\r\n=== Adapter 1 ===\r\n\r\nAdapter 'TGAC', length 4, was trimmed 15739419 times.\r\n\r\nHistogram of adapter lengths\r\nlength\tcount\r\n3\t243588\r\n4\t15495831\r\n\r\n\r\n\n=============================================================\r\n\r\nUsing version 1.2.1, I get the following:\r\n\r\ncutadapt version 1.2.1\r\nCommand line parameters: -f fastq -a TGAC -o temp_R2.fastq Output/Libraries/1c/a. R2 .fastq\r\nMaximum error rate: 10.00&#37;\r\n   No. of adapters: 1\r\n   Processed reads:     22386941\r\n   Processed bases:   1769910658 bp (1769.9 Mbp)\r\n     Trimmed reads:     14939994 (66.7&#37;)\r\n     Trimmed bases:    293854472 bp (293.9 Mbp) (16.60&#37; of total)\r\n   Too short reads:            0 (0.0&#37; of processed reads)\r\n    Too long reads:            0 (0.0&#37; of processed reads)\r\n        Total time:    764.79 s\r\n     Time per read:      0.03 ms\r\n\r\n=== Adapter 1 ===\r\n\r\nAdapter 'TGAC', length 4, was trimmed 14939994 times.\r\n\r\nNo. of allowed errors:\r\n0-4 bp: 0\r\n\r\nLengths of removed sequences\r\nlength\tcount\texpected\tmax. errors\r\n3\t223541\t349796.0\t0\r\n4\t9089680\t87449.0\t0\r\n5\t169840\t87449.0\t0\r\n6\t172085\t87449.0\t0\r\n7\t27329\t87449.0\t0\r\n8\t124616\t87449.0\t0\r\n9\t80709\t87449.0\t0\r\n10\t66715\t87449.0\t0\r\n11\t58734\t87449.0\t0\r\n12\t50558\t87449.0\t0\r\n13\t56900\t87449.0\t0\r\n14\t62381\t87449.0\t0\r\n15\t61055\t87449.0\t0\r\n16\t63647\t87449.0\t0\r\n17\t60773\t87449.0\t0\r\n18\t64370\t87449.0\t0\r\n19\t61723\t87449.0\t0\r\n20\t63820\t87449.0\t0\r\n21\t64054\t87449.0\t0\r\n22\t63128\t87449.0\t0\r\n23\t64856\t87449.0\t0\r\n24\t62749\t87449.0\t0\r\n25\t65185\t87449.0\t0\r\n26\t65380\t87449.0\t0\r\n27\t65299\t87449.0\t0\r\n28\t64298\t87449.0\t0\r\n29\t65294\t87449.0\t0\r\n30\t66493\t87449.0\t0\r\n31\t64696\t87449.0\t0\r\n32\t66269\t87449.0\t0\r\n33\t66538\t87449.0\t0\r\n34\t65602\t87449.0\t0\r\n35\t67718\t87449.0\t0\r\n36\t68825\t87449.0\t0\r\n37\t66012\t87449.0\t0\r\n38\t69049\t87449.0\t0\r\n39\t73718\t87449.0\t0\r\n40\t67470\t87449.0\t0\r\n41\t66956\t87449.0\t0\r\n42\t68519\t87449.0\t0\r\n43\t68307\t87449.0\t0\r\n44\t67932\t87449.0\t0\r\n45\t69064\t87449.0\t0\r\n46\t65439\t87449.0\t0\r\n47\t66787\t87449.0\t0\r\n48\t66954\t87449.0\t0\r\n49\t65251\t87449.0\t0\r\n50\t67843\t87449.0\t0\r\n51\t66406\t87449.0\t0\r\n52\t65572\t87449.0\t0\r\n53\t64265\t87449.0\t0\r\n54\t63502\t87449.0\t0\r\n55\t63246\t87449.0\t0\r\n56\t64259\t87449.0\t0\r\n57\t61615\t87449.0\t0\r\n58\t60848\t87449.0\t0\r\n59\t60938\t87449.0\t0\r\n60\t60028\t87449.0\t0\r\n61\t59425\t87449.0\t0\r\n62\t58737\t87449.0\t0\r\n63\t58269\t87449.0\t0\r\n64\t57147\t87449.0\t0\r\n65\t56649\t87449.0\t0\r\n66\t55557\t87449.0\t0\r\n67\t55109\t87449.0\t0\r\n68\t54932\t87449.0\t0\r\n69\t53553\t87449.0\t0\r\n70\t52342\t87449.0\t0\r\n71\t52250\t87449.0\t0\r\n72\t50597\t87449.0\t0\r\n73\t49586\t87449.0\t0\r\n74\t49801\t87449.0\t0\r\n75\t48760\t87449.0\t0\r\n76\t47626\t87449.0\t0\r\n77\t46702\t87449.0\t0\r\n78\t45693\t87449.0\t0\r\n79\t44814\t87449.0\t0\r\n80\t44731\t87449.0\t0\r\n81\t44426\t87449.0\t0\r\n82\t42597\t87449.0\t0\r\n83\t42455\t87449.0\t0\r\n84\t40958\t87449.0\t0\r\n85\t40377\t87449.0\t0\r\n86\t40518\t87449.0\t0\r\n87\t38920\t87449.0\t0\r\n88\t38541\t87449.0\t0\r\n89\t37855\t87449.0\t0\r\n90\t35991\t87449.0\t0\r\n91\t36020\t87449.0\t0\r\n92\t35596\t87449.0\t0\r\n93\t33262\t87449.0\t0\r\n94\t29560\t87449.0\t0\r\n95\t33383\t87449.0\t0\r\n96\t33456\t87449.0\t0\r\n97\t24911\t87449.0\t0\r\n98\t37085\t87449.0\t0\r\n99\t45855\t87449.0\t0\r\n100\t1108\t87449.0\t0\n\n_Original issue: http://code.google.com/p/cutadapt/issues/detail?id=61_"}}