| eb8c75d | Ivan Sovic | 26 May 2017, 00:22:05 UTC | Updated the README. | 26 May 2017, 00:22:05 UTC |
| 5f4733a | Ivan Sovic | 25 May 2017, 22:54:22 UTC | Updated the program version and the README. | 25 May 2017, 22:54:22 UTC |
| f864cb5 | Ivan Sovic | 25 May 2017, 22:54:03 UTC | Added a missing cmath include. | 25 May 2017, 22:54:03 UTC |
| af318b4 | Ivan Sovic | 25 May 2017, 22:42:12 UTC | Minor cosmetic adjustments. | 25 May 2017, 22:42:12 UTC |
| 2312af3 | Ivan Sovic | 25 May 2017, 22:24:05 UTC | Merge branch 'FixSegFault' of https://github.com/JGI-Bioinformatics/graphmap into pr1 | 25 May 2017, 22:24:05 UTC |
| d193422 | Ivan Sovic | 25 May 2017, 22:13:23 UTC | Updated seqlib. | 25 May 2017, 22:13:23 UTC |
| bab4f78 | Ivan Sovic | 25 May 2017, 22:12:22 UTC | Fixed a bug where linear anchored alignments would extend towards the left from the beginning of the reference. | 25 May 2017, 22:12:22 UTC |
| 1276b20 | Rob Egan | 21 April 2017, 01:18:23 UTC | added lower bounds check for insane alignments that start before the reference start position | 21 April 2017, 01:18:23 UTC |
| 4bda217 | Rob Egan | 21 April 2017, 00:53:51 UTC | skip alignment calculations like MD and counts when is_aligned == false | 21 April 2017, 00:53:51 UTC |
| b27145e | Rob Egan | 21 April 2017, 00:53:02 UTC | added assertion that aligment_position_start is positive | 21 April 2017, 00:53:02 UTC |
| 25f1eeb | Ivan Sovic | 05 March 2017, 00:03:48 UTC | Updated the README and the changelog. | 05 March 2017, 00:03:48 UTC |
| 9463c18 | Ivan Sovic | 04 March 2017, 21:13:45 UTC | Updated gindex to the latest version on master branch. | 04 March 2017, 21:13:45 UTC |
| c6e9f11 | Ivan Sovic | 04 March 2017, 12:46:54 UTC | Changed the program version. | 04 March 2017, 12:46:54 UTC |
| e670278 | Ivan Sovic | 04 March 2017, 12:42:35 UTC | Modified some debug output. | 04 March 2017, 12:42:35 UTC |
| 3d1f621 | Ivan Sovic | 04 March 2017, 12:05:23 UTC | Updated gindex. This version should consume less memory and be fully functional. Needs testing. | 04 March 2017, 12:05:23 UTC |
| d481a48 | Ivan Sovic | 04 March 2017, 00:32:06 UTC | Added a debug line. | 04 March 2017, 00:32:06 UTC |
| c73d519 | Ivan Sovic | 04 March 2017, 00:19:36 UTC | Testing an improved version of gindex with smaller memory consumption. | 04 March 2017, 00:19:36 UTC |
| 118c21e | Ivan Sovic | 02 March 2017, 11:44:30 UTC | Fixed the SAM header - previously forgot to trim the sequence headers to first space. | 02 March 2017, 11:44:30 UTC |
| a697f01 | Ivan Sovic | 01 March 2017, 23:22:22 UTC | Added a couple of more images, and updated the .md. | 01 March 2017, 23:22:22 UTC |
| 6ec8576 | Ivan Sovic | 01 March 2017, 22:53:24 UTC | Updated the README. | 01 March 2017, 22:53:24 UTC |
| 719bba5 | Ivan Sovic | 01 March 2017, 22:49:53 UTC | Added an initial description of the RNA-seq alignment progress and experimental approaches. | 01 March 2017, 22:49:53 UTC |
| 0faea9c | Ivan Sovic | 01 March 2017, 21:11:42 UTC | Testing without conversion from unique_ptr to shared_ptr. | 01 March 2017, 21:11:42 UTC |
| fe272f9 | Ivan Sovic | 28 February 2017, 19:26:07 UTC | Updated the README. | 28 February 2017, 19:26:07 UTC |
| ecffdf4 | Ivan Sovic | 28 February 2017, 18:39:26 UTC | Updated README, the changelog and a name of a command line parameter. | 28 February 2017, 18:39:26 UTC |
| c02db15 | Ivan Sovic | 26 February 2017, 20:50:19 UTC | Added two clears. | 26 February 2017, 20:50:19 UTC |
| d77a829 | Ivan Sovic | 25 February 2017, 21:23:10 UTC | Fixed debug output. | 25 February 2017, 21:23:10 UTC |
| a963926 | Ivan Sovic | 25 February 2017, 21:18:33 UTC | Small modifications. Was testing for memory leaks, tested on an imput of 10000 same reads, and memory seems stable. | 25 February 2017, 21:18:33 UTC |
| d61ac06 | Ivan Sovic | 23 February 2017, 15:39:59 UTC | Re-implemented BuildIndex. Added a parameter --auto-build-index which will cause the index to be rebuilt only if the existing index file is of an older version or corrupt. If not specified, the rebuilding process will not commence automatically. | 23 February 2017, 15:39:59 UTC |
| d512546 | Ivan Sovic | 23 February 2017, 11:08:49 UTC | Removed some old heuristics for checking overlap validity. Also, in the previous commit new parameters were added to allow command line modification of overlap filtering thresholds. | 23 February 2017, 11:08:49 UTC |
| f305c20 | Ivan Sovic | 23 February 2017, 11:05:04 UTC | Updated BuildIndex in Owler to rebuild the index if the version is wrong, and also only if a parameter --rebuild-index is specified. Updated gindex to allow for not asserting when loading the index. | 23 February 2017, 11:05:04 UTC |
| f6dbbd1 | Ivan Sovic | 23 February 2017, 08:19:12 UTC | Updated the filtering heuristics to achieve higher precision. Need to add several commandline parameters: heuristics values and index storing/loading modifications. | 23 February 2017, 08:19:12 UTC |
| fbb9758 | Ivan Sovic | 22 February 2017, 09:12:47 UTC | Fixed an issue with anchored alignment of the back of a read. | 22 February 2017, 09:12:47 UTC |
| 60d84b7 | Ivan Sovic | 20 February 2017, 17:03:02 UTC | I noticed that the number of seeds which passed LCSk was significantly lower than that of Minimap in it's output PAF file. I inspected, and it seems that the problem was in that, that LCSk (of course) didn't pick overlapping k-mers, which reduced their number significantly, and the overall final score. I introduced a hack which runs LCSk for k = 1, and then calculates the number of covered bases. | 20 February 2017, 17:03:02 UTC |
| 5a2fe1d | Ivan Sovic | 20 February 2017, 14:03:22 UTC | Fixed an issue with the default value of --shape. It was undefined before, and did not work well unless specified (well duh). | 20 February 2017, 14:03:22 UTC |
| 53c912b | Ivan Sovic | 20 February 2017, 11:04:01 UTC | Updated the version in program_parameters. | 20 February 2017, 11:04:01 UTC |
| 00a77c8 | Ivan Sovic | 20 February 2017, 10:42:35 UTC | Updated gindex. | 20 February 2017, 10:42:35 UTC |
| 4acd691 | Ivan Sovic | 20 February 2017, 10:02:07 UTC | Moved the sort to the GenerateOutput_ function to ensure that everything is in the right order. | 20 February 2017, 10:02:07 UTC |
| 6a35bc3 | Ivan Sovic | 20 February 2017, 10:00:00 UTC | Filtered duplicate overlaps (e.g. forward and reverse strand, only the best one is left). | 20 February 2017, 10:00:00 UTC |
| fc3bdbd | Ivan Sovic | 19 February 2017, 23:12:41 UTC | Experimenting with overlap filtering heuristics. | 19 February 2017, 23:12:41 UTC |
| ea5758d | Ivan Sovic | 19 February 2017, 22:43:07 UTC | Testing a different modification, CheckOverlapV3_. | 19 February 2017, 22:43:07 UTC |
| b5517a4 | Ivan Sovic | 19 February 2017, 17:32:28 UTC | Shapes can now be specified via commandline for Owler. | 19 February 2017, 17:32:28 UTC |
| 930b04d | Ivan Sovic | 19 February 2017, 15:30:49 UTC | Fixed the time and memory measurements for Owler. | 19 February 2017, 15:30:49 UTC |
| c8eb1fa | Ivan Sovic | 19 February 2017, 14:27:51 UTC | Rearranged some Owler code to be nicer. This commit produces a single contig assembly using Miniasm on ecoli_map006_ont data. | 19 February 2017, 14:27:51 UTC |
| 7aa18f0 | Ivan Sovic | 19 February 2017, 12:24:56 UTC | Cleaned up some temp stuff. | 19 February 2017, 12:24:56 UTC |
| ced7942 | Ivan Sovic | 19 February 2017, 11:10:23 UTC | Reverted back to the code from one commit before - there were some problems with the new approach. Working now on trying to increase recall, which requires messing with LCSk filtering functions and CheckOverlap_. | 19 February 2017, 11:10:23 UTC |
| 4dbe48c | Ivan Sovic | 18 February 2017, 19:36:17 UTC | Testing a new approach for collecting hits which preallocates memory for each thread. | 18 February 2017, 19:36:17 UTC |
| 46a4cff | Ivan Sovic | 18 February 2017, 18:46:24 UTC | Changed the call to CheckAlignmentSane, instead of the elaborate reference id expression, there is now a value of abs_ref_id passed as an argument. There was a problem on some reads on S. Cerevisiae, where the alignments are wrongly cut. | 18 February 2017, 18:46:24 UTC |
| 888b46f | Ivan Sovic | 18 February 2017, 18:33:59 UTC | Changed the core_graphmap part for seed lookup which calls the index function which copies seeds. Now lookup is performed directly. | 18 February 2017, 18:33:59 UTC |
| 2562bdd | Ivan Sovic | 18 February 2017, 16:07:00 UTC | Reverted back to some debug info when aligning reads. | 18 February 2017, 16:07:00 UTC |
| 63cd51b | Ivan Sovic | 18 February 2017, 13:07:23 UTC | Fixed an important warning where a value of a variable was dependant on the exact same variable when being defined. | 18 February 2017, 13:07:23 UTC |
| a9fd402 | Ivan Sovic | 18 February 2017, 13:05:22 UTC | Added support for MHAP output, and made it the default format. Fixed some debug output for when inspecting a particular read. | 18 February 2017, 13:05:22 UTC |
| b1c7487 | Ivan Sovic | 17 February 2017, 14:12:37 UTC | Removed multiplies for scores when using minimizer_windows. | 17 February 2017, 14:12:37 UTC |
| 6fd3364 | Ivan Sovic | 17 February 2017, 11:39:57 UTC | Working on Owler. This version should be functional, but it should be optimized for speed. Also, experimenting with different shapes needs to be done. One thing I learned - indexing with a minimizer of one shape and looking up with a minimizer of several lookup shapes yields bad results, which makes sense when I think about it afterwards. | 17 February 2017, 11:39:57 UTC |
| 613448c | Ivan Sovic | 16 February 2017, 13:26:27 UTC | Working on a new version of Owler. | 16 February 2017, 13:26:27 UTC |
| 0ef4d8e | Ivan Sovic | 15 February 2017, 09:25:57 UTC | Working on Owler. Does not compile currently. | 15 February 2017, 09:25:57 UTC |
| 03b8466 | Ivan Sovic | 14 February 2017, 17:03:32 UTC | Fixed the issue with circular alignment of the front of the read, it should now work fine. I would still like to run more profiling. I also found and fixed a memory leak when splitting the circular alignments as well. Also, fixed the issue of empty lines when the circular alignment is applied. | 14 February 2017, 17:03:32 UTC |
| 0efa61f | Ivan Sovic | 14 February 2017, 11:12:37 UTC | Changed debug output and updated gindex to better handle count cutoff. | 14 February 2017, 11:12:37 UTC |
| e801b32 | Ivan Sovic | 14 February 2017, 10:05:28 UTC | Changed debug output. | 14 February 2017, 10:05:28 UTC |
| ef30edb | Ivan Sovic | 13 February 2017, 14:40:29 UTC | Changed the command line. Minimizers and thresholding are now applied by default. It can be turned off individually by tuning --minimizer-window and --threshold-hits parameters, or by using -x sensitive. | 13 February 2017, 14:40:29 UTC |
| 331d158 | Ivan Sovic | 12 February 2017, 23:43:25 UTC | Fixed the issue where a number of transcriptome alignments would for some reason be called erroneous. The problem was that I was checking the sanity of alignment *after* the alignment was modified with 'N' CIGAR operations. | 12 February 2017, 23:43:25 UTC |
| c92c7cf | Ivan Sovic | 12 February 2017, 18:58:47 UTC | Removed some debug output from the index. | 12 February 2017, 18:58:47 UTC |
| b2e5540 | Ivan Sovic | 12 February 2017, 18:53:15 UTC | Fixed a bug recently introduced in transcriptome construction, where the absolute sequence id was never initialized. This caused problems when building the index. | 12 February 2017, 18:53:15 UTC |
| 4524807 | Ivan Sovic | 12 February 2017, 13:53:51 UTC | Finished the BuildIndex method so that it can load/store the index to file. MinimizerIndex now provides these functionalities. Added an option 'fly-index' which allows to build the index on the fly instead of storing it to file. However, if the index already exists on the disk, it will be loaded unless --rebuild-index is specified, which makes everything work on the fly. Removed an old parameter max_num_hits which no longer makes sense provided that MinimizerIndex has it's own count threshold cutoff. | 12 February 2017, 13:53:51 UTC |
| e406f0d | Ivan Sovic | 11 February 2017, 21:50:26 UTC | Reverted back to old region selection and ProcessRead_ for now, until I finish the MinimizerIndex implementation. | 11 February 2017, 21:50:26 UTC |
| 8128059 | Ivan Sovic | 11 February 2017, 21:16:08 UTC | Working on a new version of region selection which would depend on thresholding the counts, and then just compiling all hits in a single vector instead of binning. The binning process is extremely on large references and short reads. | 11 February 2017, 21:16:08 UTC |
| c419c6a | Ivan Sovic | 09 February 2017, 15:28:27 UTC | Added initial support for seed hit thresholding. | 09 February 2017, 15:28:27 UTC |
| fe50124 | Ivan Sovic | 09 February 2017, 00:30:03 UTC | Modified a HUGE amount of code to replace the index. Temporarily removed Owler until I test GraphMap, I will put it back eventually. The new index is implemented as part of the codebase, in the gindex repository. The index is now multithreaded, much faster, and even allows minimizers. Everything needs thorough testing. I reckon I could compare the output to previous releases using a simple Venn comparison. | 09 February 2017, 00:30:03 UTC |
| 7609fe6 | Ivan Sovic | 06 February 2017, 22:07:14 UTC | Fixed some bugs (potential memory leaks) in index_hash.cc and alignment_wrappers.cc, and added some debug code in anchored.cc and index_spaced_hash_fast.cc. | 06 February 2017, 22:07:14 UTC |
| 059060a | Ivan Sovic | 05 February 2017, 19:03:40 UTC | Debugging the crash on hg19. | 05 February 2017, 19:03:40 UTC |
| 8881fa2 | Ivan Sovic | 04 February 2017, 16:53:31 UTC | Added some debug output. | 04 February 2017, 16:53:31 UTC |
| 5a831a0 | Ivan Sovic | 04 February 2017, 14:57:50 UTC | Cleaning the IndexSpacedHashFast and debugging. | 04 February 2017, 14:57:50 UTC |
| b1672ae | Ivan Sovic | 01 February 2017, 12:17:39 UTC | Debugging an invalid read address in index_spaced_hash_fast, line 520 in the previous commit. | 01 February 2017, 12:17:39 UTC |
| 84f058f | Ivan Sovic | 28 January 2017, 10:34:46 UTC | Minor changes to verbose output. | 28 January 2017, 10:34:46 UTC |
| e55a18c | Ivan Sovic | 27 January 2017, 23:52:18 UTC | v0.4.0 -> v0.4.1 | 27 January 2017, 23:52:18 UTC |
| 6f58139 | Ivan Sovic | 27 January 2017, 23:06:29 UTC | Fixed the SAM headers for when mapping to a transcriptome. | 27 January 2017, 23:06:29 UTC |
| 6a4f0f1 | Ivan Sovic | 22 January 2017, 15:23:30 UTC | Updated the README. | 22 January 2017, 15:23:30 UTC |
| 89b31e8 | Ivan Sovic | 22 January 2017, 15:18:59 UTC | Updated the README. | 22 January 2017, 15:18:59 UTC |
| c644f60 | Ivan Sovic | 22 January 2017, 14:16:03 UTC | 0.3.2 -> v0.4.0. Updated the README. | 22 January 2017, 14:16:03 UTC |
| 19cb38c | Ivan Sovic | 22 January 2017, 01:37:08 UTC | Fixed a bug in MD generation for the first operation. Updated Edlib in seqlib to use the correct free instead of a delete. MD in semiglobal alignment was also faulty, fixed that as well. | 22 January 2017, 01:37:08 UTC |
| 47d8879 | Ivan Sovic | 21 January 2017, 15:11:42 UTC | Updated Seqlib to the version with Edlib which has a bugfix for 1X instead of 1=. | 21 January 2017, 15:11:42 UTC |
| 6d8f141 | Ivan Sovic | 19 January 2017, 17:38:48 UTC | Tested the previous commit on several reads and checked the error rates, it seems to be fine. Also, removed some debug output. | 19 January 2017, 17:38:48 UTC |
| 5f363a0 | Ivan Sovic | 19 January 2017, 17:27:47 UTC | Fixed the D's before S's (and/or after). Testing needed. | 19 January 2017, 17:27:47 UTC |
| 68222a3 | Ivan Sovic | 19 January 2017, 13:48:11 UTC | Fixed the mapping to transcriptomes generated from reverse-complement strand of the input genome. | 19 January 2017, 13:48:11 UTC |
| b6a4d99 | Ivan Sovic | 18 January 2017, 13:32:26 UTC | Handled an edge case where the input FASTA/FASTQ file of reads actually has sequences of size 0. | 18 January 2017, 13:32:26 UTC |
| 97ca145 | Ivan Sovic | 17 January 2017, 13:49:40 UTC | Fixed the basic CIGAR for transcriptome. | 17 January 2017, 13:49:40 UTC |
| 3268c14 | Ivan Sovic | 17 January 2017, 13:00:19 UTC | Testing the transcriptome mapping. | 17 January 2017, 13:00:19 UTC |
| d1bdc48 | Ivan Sovic | 17 January 2017, 11:03:08 UTC | Handled a special case when GTF file is faulty and there are multiple same TIDs on several different chromosomes, which shouldn't be possible. | 17 January 2017, 11:03:08 UTC |
| 1a4ef3e | Ivan Sovic | 16 January 2017, 15:58:58 UTC | Fixed the transcriptome/genome index creation. Updated the index version. | 16 January 2017, 15:58:58 UTC |
| 5f1699d | Ivan Sovic | 16 January 2017, 11:12:41 UTC | Fixed a bug when anchored aligning the beginning of the read and there is an overhang from the query. The starting position for the alignment was wrong. Should be ok now. | 16 January 2017, 11:12:41 UTC |
| 8bdc221 | Ivan Sovic | 13 January 2017, 14:53:39 UTC | Handled updating of the ref_start and ref_header for transforming from transcriptome to genome space. Also, debugged the MD conversion function, there was an invalid read and potential memory leaks. Everything needs thorough testing. | 13 January 2017, 14:53:39 UTC |
| 368a3d8 | Ivan Sovic | 12 January 2017, 16:10:23 UTC | I implemented the conversion from the transcriptome space to the genome space, hopefully it's working now. | 12 January 2017, 16:10:23 UTC |
| 94fc7ba | Ivan Sovic | 11 January 2017, 22:13:39 UTC | Working on adding the 'N's. | 11 January 2017, 22:13:39 UTC |
| ac29d55 | Ivan Sovic | 11 January 2017, 16:04:50 UTC | Working on adding the N bases in the transcriptome mapping. | 11 January 2017, 16:04:50 UTC |
| fb99a57 | Ivan Sovic | 05 January 2017, 17:08:20 UTC | Working on moving from transcriptome space to genome space. | 05 January 2017, 17:08:20 UTC |
| bbdf9e3 | Ivan Sovic | 04 January 2017, 16:04:36 UTC | This commit and the previous commit won't compile. | 04 January 2017, 16:04:36 UTC |
| 070cdaa | Ivan Sovic | 04 January 2017, 16:03:47 UTC | Added a placeholder for conversion from transcriptome space to genome space. | 04 January 2017, 16:03:47 UTC |
| 70ec87a | Ivan Sovic | 04 January 2017, 14:42:16 UTC | Fixed the fwd/rev MHAP output in the align -x overlap mode. | 04 January 2017, 14:42:16 UTC |
| 17a86b4 | Ivan Sovic | 04 January 2017, 14:27:16 UTC | Fixed the second segfault in Issue #43. There were subtile index out of bounds errors due to indexing shapes (don't care position actually extend the shape beyond it's predefined number of bases). Interesting that this didn't manifest before, especially on larger genomes. | 04 January 2017, 14:27:16 UTC |
| 7ab6bbb | Ivan Sovic | 03 January 2017, 15:58:46 UTC | Added an initial (yet completely untested) MHAP output format for the align mode. Reworked the make_transcript a bit to store the GTF info in the index, which should allow for reverse transformation from transcriptome space to genome space. | 03 January 2017, 15:58:46 UTC |
| ce36440 | Ivan Sovic | 02 January 2017, 08:40:26 UTC | Merge branch 'dev' into trans | 02 January 2017, 08:40:26 UTC |
