Bug in the sampler

[massyah]

Understand why the sample C_SYNTHP53_13643_1000_50_3_1-1-1 doesn't have the alteration that C_SYNTHP53_13643_700_50_3_1-1-1 has We should find the (injected and altered) k-mer TCCCCAGCCAAAGAAGAC in both files, but it's completely missing in the sample with 1000 reads => micado doesn't find it.

[massyah]

Grep shows that the altered k-mer is missing in several samples with 50% alterations:

grep "TCCCCAGCCAAAGAAGAC" data/synthetic/reads/13643 -l data/synthetic/reads/C_SYNTHP53_13643_1000_035_1_1-1-1.fastq data/synthetic/reads/C_SYNTHP53_13643_1000_035_2_1-1-1.fastq data/synthetic/reads/C_SYNTHP53_13643_1000_035_3_1-1-1.fastq data/synthetic/reads/C_SYNTHP53_13643_1000_040_1_1-1-1.fastq [...]

[massyah]

Analysis of the log of the sampler shows that as we increase the coverage, we increase the probability of picking reads mapping outside the region of interest, e.g. for 13643:

exec_logs/sampler_log_C_SYNTHP53_13643_1000_035_1_1-1-1.txt:2015-11-24 23:03:48,398 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_035_2_1-1-1.txt:2015-11-24 23:12:01,721 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_035_3_1-1-1.txt:2015-11-24 23:08:18,461 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_040_1_1-1-1.txt:2015-11-24 23:06:28,524 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_040_2_1-1-1.txt:2015-11-24 23:08:50,392 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_040_3_1-1-1.txt:2015-11-24 23:15:48,883 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_045_1_1-1-1.txt:2015-11-24 23:05:49,408 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_045_2_1-1-1.txt:2015-11-24 23:02:48,571 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_045_3_1-1-1.txt:2015-11-24 23:09:44,280 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_05_1_1-1-1.txt:2015-11-24 23:11:26,692 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_05_2_1-1-1.txt:2015-11-24 23:05:17,882 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_05_3_1-1-1.txt:2015-11-24 23:03:18,633 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_1000_10_1_1-1-1.txt:2015-11-24 23:15:07,383 - READSAMPLER - INFO - Will sample between 803 and 1838 exec_logs/sampler_log_C_SYNTHP53_13643_1000_10_2_1-1-1.txt:2015-11-24 23:02:52,669 - READSAMPLER - INFO - Will sample between 803 and 1838 exec_logs/sampler_log_C_SYNTHP53_13643_1000_10_3_1-1-1.txt:2015-11-24 23:11:55,515 - READSAMPLER - INFO - Will sample between 803 and 1838 exec_logs/sampler_log_C_SYNTHP53_13643_1000_50_1_1-1-1.txt:2015-11-24 23:07:10,597 - READSAMPLER - INFO - Will sample between 801 and 1838 exec_logs/sampler_log_C_SYNTHP53_13643_1000_50_2_1-1-1.txt:2015-11-24 23:13:20,414 - READSAMPLER - INFO - Will sample between 801 and 1838 exec_logs/sampler_log_C_SYNTHP53_13643_1000_50_3_1-1-1.txt:2015-11-24 23:11:54,097 - READSAMPLER - INFO - Will sample between 801 and 1838 exec_logs/sampler_log_C_SYNTHP53_13643_150_035_1_1-1-1.txt:2015-11-24 23:09:42,442 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_035_2_1-1-1.txt:2015-11-24 23:05:47,662 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_035_3_1-1-1.txt:2015-11-24 23:13:23,116 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_040_1_1-1-1.txt:2015-11-24 23:12:21,061 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_040_2_1-1-1.txt:2015-11-24 23:06:46,324 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_040_3_1-1-1.txt:2015-11-24 23:10:31,455 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_045_1_1-1-1.txt:2015-11-24 23:03:55,751 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_045_2_1-1-1.txt:2015-11-24 23:04:52,571 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_045_3_1-1-1.txt:2015-11-24 23:06:39,648 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_05_1_1-1-1.txt:2015-11-24 23:07:33,128 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_05_2_1-1-1.txt:2015-11-24 23:06:41,331 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_05_3_1-1-1.txt:2015-11-24 23:03:50,624 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_10_1_1-1-1.txt:2015-11-24 23:12:12,649 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_10_2_1-1-1.txt:2015-11-24 23:11:33,282 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_10_3_1-1-1.txt:2015-11-24 23:08:17,742 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_50_1_1-1-1.txt:2015-11-24 23:10:55,358 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_50_2_1-1-1.txt:2015-11-24 23:15:32,128 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_150_50_3_1-1-1.txt:2015-11-24 23:05:03,827 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_035_1_1-1-1.txt:2015-11-24 23:06:56,373 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_035_2_1-1-1.txt:2015-11-24 23:08:25,322 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_035_3_1-1-1.txt:2015-11-24 23:12:11,207 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_040_1_1-1-1.txt:2015-11-24 23:04:54,085 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_040_2_1-1-1.txt:2015-11-24 23:05:51,849 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_040_3_1-1-1.txt:2015-11-24 23:08:13,583 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_045_1_1-1-1.txt:2015-11-24 23:05:20,378 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_045_2_1-1-1.txt:2015-11-24 23:13:45,116 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_045_3_1-1-1.txt:2015-11-24 23:11:42,003 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_05_1_1-1-1.txt:2015-11-24 23:14:31,646 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_05_2_1-1-1.txt:2015-11-24 23:05:35,399 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_05_3_1-1-1.txt:2015-11-24 23:14:07,620 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_10_1_1-1-1.txt:2015-11-24 23:13:58,909 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_10_2_1-1-1.txt:2015-11-24 23:06:51,926 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_10_3_1-1-1.txt:2015-11-24 23:14:12,171 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_500_50_1_1-1-1.txt:2015-11-24 23:09:01,358 - READSAMPLER - INFO - Will sample between 803 and 1238 exec_logs/sampler_log_C_SYNTHP53_13643_500_50_2_1-1-1.txt:2015-11-24 23:14:18,958 - READSAMPLER - INFO - Will sample between 803 and 1238 exec_logs/sampler_log_C_SYNTHP53_13643_500_50_3_1-1-1.txt:2015-11-24 23:09:05,986 - READSAMPLER - INFO - Will sample between 803 and 1238 exec_logs/sampler_log_C_SYNTHP53_13643_700_035_1_1-1-1.txt:2015-11-24 23:05:46,351 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_035_2_1-1-1.txt:2015-11-24 23:07:40,720 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_035_3_1-1-1.txt:2015-11-24 23:10:00,400 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_040_1_1-1-1.txt:2015-11-24 23:08:40,592 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_040_2_1-1-1.txt:2015-11-24 23:15:20,234 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_040_3_1-1-1.txt:2015-11-24 23:13:47,712 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_045_1_1-1-1.txt:2015-11-24 23:08:24,551 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_045_2_1-1-1.txt:2015-11-24 23:12:41,146 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_045_3_1-1-1.txt:2015-11-24 23:04:50,055 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_05_1_1-1-1.txt:2015-11-24 23:15:49,762 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_05_2_1-1-1.txt:2015-11-24 23:13:06,948 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_05_3_1-1-1.txt:2015-11-24 23:06:53,080 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_10_1_1-1-1.txt:2015-11-24 23:06:30,928 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_10_2_1-1-1.txt:2015-11-24 23:09:08,884 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_10_3_1-1-1.txt:2015-11-24 23:13:29,926 - READSAMPLER - INFO - Will sample between 803 and 1237 exec_logs/sampler_log_C_SYNTHP53_13643_700_50_1_1-1-1.txt:2015-11-24 23:14:31,781 - READSAMPLER - INFO - Will sample between 801 and 1238 exec_logs/sampler_log_C_SYNTHP53_13643_700_50_2_1-1-1.txt:2015-11-24 23:06:08,475 - READSAMPLER - INFO - Will sample between 801 and 1238 exec_logs/sampler_log_C_SYNTHP53_13643_700_50_3_1-1-1.txt:2015-11-24 23:06:22,885 - READSAMPLER - INFO - Will sample between 801 and 1238

[JRudewicz]

The sampler method has change. We now sample in each real sample and not in a big bulk sample resulting from the merge of all samples as previously.