I hereby claim:
- I am mp15 on github.
- I am technicalvault (https://keybase.io/technicalvault) on keybase.
- I have a public key ASCKvWAVYpBBTycEJ1oXFWnyoLJh_dtreq6UtYZ8YKdiTAo
To claim this, I am signing this object:
Martin Pollard mp15
mp15
/ cram_opt.patch
Created
August 11, 2015 16:15
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| diff --git a/bam_addrprg.c b/bam_addrprg.c | |
| index 5343dcd..941ecd3 100644 | |
| --- a/bam_addrprg.c | |
| +++ b/bam_addrprg.c | |
| @@ -24,6 +24,7 @@ DEALINGS IN THE SOFTWARE. */ | |
| #include <htslib/sam.h> | |
| #include "samtools.h" | |
| +#include "sam_opts.h" | |
| #include <string.h> |
mp15
/ testcase1.sam
Last active
May 16, 2016 16:23
SKBR3 Data that induces alpha/beta error in PacBio CCS
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| @HD VN:1.5 SO:unknown pb:3.0.2 | |
| @RG ID:b22e801c PL:PACBIO DS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.1.142990;FRAMERATEHZ=75.000000 PU:m150517_204412_sherri_c100800262550000001823168409091511_s1_p0 PM:RS | |
| @PG ID:bax2bam-0.0.8 PN:bax2bam VN:0.0.8 DS:bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format. CL:bax2bam m150517_204412_sherri_c100800262550000001823168409091511_s1_p0.bas.h5 | |
| m150517_204412_sherri_c100800262550000001823168409091511_s1_p0/101288/14128_16134 4 * 0 255 * * 0 0 GCGCCTGTCCCTACCACTGGAGCAACATACACTATCTCACCTAAACCTACACCTAGTGACTTGGCTTTTTCACAGCCTCTTGTCTTGTGCTTCTCTACCTTTTTGGTTCAATCTTCCTTCTCTTCTACTTCTTTTTTTTTTTATGAAGTTTTTATGAAAGCCTTGCCTTCGCCCAGGCTGGAGTGCAGTGGCACATCTCAGCTCACTGGCAACCTCAAGTCCTTCCCGGGTTCGCAAGGGCTTCTCTTGCCTCAAGTCCTCTTAGGTAGCTGGGATTACAGGTGCCCACCACCACACCCAGCTAAATTTTTTGTACTTTTAGTAGAGATGGGGTTTTTGCCATGGTTGTCTGGCTGGGTCTCGAACTCCTG |
mp15
/ fc_run.cfg
Last active
January 9, 2019 16:10
FALCON config for HGAP 4 002032/tasks/falcon_ns.tasks.task_falcon_gen_config-0/fc_run.cfg vs. FALCON conda fc_run_human.15kb.tweaked.cfg (in theory should be functionally the same)
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| [General] | |
| genome_size = 3200000000 | |
| pbsmrtpipe.hgap_aggressiveasm_bool = False | |
| falcon_sense_greedy = False | |
| falcon_sense_skip_contained = False | |
| length_cutoff = -1 | |
| pbsmrtpipe.hgap_genomelength_str = 3200000000 | |
| pa_dbsplit_option = -a -x500 -s400 | |
| ovlp_hpcdaligner_option = -v -dal128 -M24 -k24 -h1024 -e.96 -l2500 -s100 | |
| seed_coverage = 30.0 |
mp15
/ fc_run.cfg
Created
January 9, 2019 15:30
002032/tasks/falcon_ns.tasks.task_falcon_gen_config-0/fc_run.cfg
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| [General] | |
| genome_size = 3200000000 | |
| pbsmrtpipe.hgap_aggressiveasm_bool = False | |
| falcon_sense_greedy = False | |
| falcon_sense_skip_contained = False | |
| length_cutoff = -1 | |
| pbsmrtpipe.hgap_genomelength_str = 3200000000 | |
| pa_dbsplit_option = -a -x500 -s400 | |
| ovlp_hpcdaligner_option = -v -dal128 -M24 -k24 -h1024 -e.96 -l2500 -s100 | |
| seed_coverage = 30.0 |
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| NC_000001.11 chr1 | |
| NC_000002.12 chr2 | |
| NC_000003.12 chr3 | |
| NC_000004.12 chr4 | |
| NC_000005.10 chr5 | |
| NC_000006.12 chr6 | |
| NC_000007.14 chr7 | |
| NC_000008.11 chr8 | |
| NC_000009.12 chr9 | |
| NC_000010.11 chr10 |