pristine:0000000095-49c6411ce78bfea8e8f8ee25748de4c6f7147fbfce8eea44ef2e9fb3f759bc2a [initial version Ketil Malde **20110607111752 Ignore-this: 4d81bc6aa8821ac448371bb15fd6b605 ] hash: 0000002380-3b1781da7dab7ba06ae36c484b50f215c4b4ace248cfced2a6e04ce328dd6cc4 [Small fixes, add /1 or /2 to read names. Ketil Malde **20110607112552 Ignore-this: 391e4cf1328e7ebace665f734424ec63 ] hash: 0000000582-e2d69a4f97032d83f0562aeb4b17720674c9d2c2ee37eb816533ae462b2e4816 [Use global caches for unmatched reads. Ketil Malde **20110608114111 Ignore-this: 7889ca1b95c5bdb71f9d5e731f065ef Ideally, these should all match up, but in practice... This way, we ensure that we only ever write out matched pairs of reads. ] hash: 0000002449-aae4d86074d82e18405f41d6a810a986b3a6fdfd875901a9624b5bb130e0e548 [combine read/lookup operations Ketil Malde **20110609100050 Ignore-this: 8cf7d6fe3a7c284b4dd46624778e4a0f ] hash: 0000000536-4eeab141cad4679c0bd8c4d36adc3694ab216eb593a6c89afc17e5ae0cc43445 [proper naming Ketil Malde **20110609113737 Ignore-this: ce8b774950aa499a5fdb9a8a05a8f912 ] hash: 0000000139-4bf969fa82ba02d7c9e4cdc9892f0cfb465cdd3f11f8dcd6a0a8f70f936ea017 [add quality output Ketil Malde **20110816124909 Ignore-this: 2e1eafb8dd47bf91c491e7f0f58228ca ] hash: 0000000469-ba63b64c9adca65927f5503fc7cd093d07907672340f7d6fe56c0999a07217ac [Merge hPuts into formatFq - no (big) improvement. Ketil Malde **20110816133451 Ignore-this: 6849ac6fbb9e632881dcfc1c933b6a4 ] hash: 0000000852-39d8273cd23c1ad8aced015bb85d3e3872b4bd43e63e63fbcb64e0addae72c5e [Avoid extracting data from each Bam1 more than once. Ketil Malde **20110816133540 Ignore-this: fc33e30cd8191ccf79d4b27f1b8ec4bf Still most of the time goes to GC. ] hash: 0000003782-93871344b6fa968d8d920750109fc3fffec2a993da116b563ebd435e79dc6600 [factor out extraction Ketil Malde **20110816205728 Ignore-this: adaf6416635fcd0babd576d321ae541c ] hash: 0000001058-6ae19caed46d574af4bc30eda9c80f8d61a5e4dd30a43f70ed8f6e06982aec73 [Use tuples instead of lists. Ketil Malde **20110817124326 Ignore-this: 16cbb02c387ee483582077b797dcf3e ] hash: 0000002274-1126263f9a7cdc308248a68aae4271e7b97bebdc9151a151a9f6416254f92b9e [Warning fixes Ketil Malde **20110817124335 Ignore-this: 9c98fcd690090846c3e1e3a0c350edce ] hash: 0000000404-7aa7f2363eb894ce41eb9982007a07c076a8c2e37ee29be195a689b407107bef