annotate conc.awk @ 135:21bb464c1d53 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 78bf7abb931bf3d348837c7211cd3cff32486691

#!/bin/awk -f
# input must be paf
# pipe to sort -n -r -k2
# few duplicates in a 14M row paf converted from a paired bam from VGP mUroPar1
{
    if (($1,$3,$6,$8) in concordance)
        { concordance[$1,$3,$6,$8]++ }
    else
        { concordance[$1,$3,$6,$8] = 1 }
 }
 END {
    for (k in concordance) {print k, concordance[k]}
 }




## PAF specification
## 
## Col	Type	Description
## 1	string	Query sequence name
## 2	int	Query sequence length
## 3	int	Query start (0-based)
## 4	int	Query end (0-based)
## 5	char	Relative strand: "+" or "-"
## 6	string	Target sequence name
## 7	int	Target sequence length
## 8	int	Target start on original strand (0-based)
## 9	int	Target end on original strand (0-based)
## 10	int	Number of residue matches
## 11	int	Alignment block length
## 12	int	Mapping quality (0-255; 255 for missing)
## 
## 
## chr10	135711693	0	410000	+	chr10	135912142	60	410218	18	410158	32	id:f:0.999395	kc:f:1.01221
## chr10	135711693	415000	1305000	+	chr10	135912142	412798	1295808	17	890000	28	id:f:0.998493	kc:f:0.971423
## chr10	135711693	1310000	2395000	+	chr10	135912142	1300732	2385827	15	1085095	30	id:f:0.998896	kc:f:1.02767
## chr10	135711693	2400000	25440000	+	chr10	135912142	2385341	25429367	18	23044026	29	id:f:0.998716	kc:f:1.04082
## chr10	135711693	25445000	26735000	+	chr10	135912142	25429997	26720864	13	1290867	28	id:f:0.998239	kc:f:1.05397
## chr10	135711693	26740000	37190000	+	chr10	135912142	26722183	37175820	20	10453637	29	id:f:0.998842	kc:f:1.0341
## chr10	135711693	37185000	37195000	-	chr10	135912142	37175523	37185020	13	10000	22	id:f:0.993765	kc:f:1.02691
## chr10	135711693	37195000	37285000	+	chr10	135912142	37181742	37271716	18	90000	27	id:f:0.998021	kc:f:1.02883
## chr10	135711693	37285000	38650000	+	chr10	135912142	37283684	38647751	18	1365000	33	id:f:0.999466	kc:f:1.03306
## 
## #E00526:120:HYYLYCCXY:8:1206:18842:33182 179 chr10:0-100000H1 23129 0 150M chr11:0-100000H2 88118 0 
## #ATTATCTCAGCAGATGCAGAAAAGGCCTTCAATAAAAGACAACACCCCTTCAGGTTAAAAACACTCAATTAACTAGGTGTTCATGGGACATACCTCAAAATAATAAGAGCCATTTATGACAAACCCACAGACAATATCATGCTGAATGGG 
## #<<F7---<<JJJFJJF-7<FFJAA7A--<<F<-A7AAA-<F777--F<-77<F--7A-AAJA-<-JJ-JFFA<-<<JAJFF<FF--AJF7FFJ<-JJFFJ7F--AA--J<F-A<JF7<AFFF-<<<FAFF-AFA7F-JF7FJAJJF<AA< NM:i:19 MD:Z:9A28T5T7T2C6T6A6C1A2G1A2A0T2C21C0A16C9A7A1 AS:i:58 
## #XS:i:58 XA:Z:chr10:0-100000H2,-22753,150M,19;chr14:0-100000H1,+33583,150M,19;chr13:0-100000H1,+48625,150M,19;chr13:0-100000H2,+35689,150M,20; E00526:120:HYYLYCCXY:8:2223:11495:36241 147 chr10:0-100000H1 30113 0 150M 
## #chr10:0-100000H2 29642 0 AGAGCGCCTCTCCTCCTCCAAAGGAACACAGTTCCTCACCAGCAACAGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAACTACTCCGAGCTACAGGAGGAAATTCAAACCAAAGGCAAAC 
## #-<A-FF7--7-<7-A-AJJJAF7JJJFAA-FF-AFFFJJJFJJJFFAAAFJAJJJFJJJJFJFJA7AAFJF<<<A<JF7FJAAAFJJ<JJJ7<JJJJAAJJJFJJFJF<<F7JAAJJFJFJJ<AJAFJJJJJJAJJ7AJF<<-AFFF<A< NM:i:13 MD:Z:26T0G17T0G13T6C11A0C28T5T7G6C18G0 AS:i:89 XS:i:89 
## #XA:Z:chr10:0-100000H2,-29737,150M,13; ...
## #columns: readID chr1 pos1 chr2 pos2 strand1 strand2
## #EAS139:136:FC706VJ:2:2104:23462:197393 chr1 10000 chr1 20000 + +
## #EAS139:136:FC706VJ:2:8762:23765:128766 chr1 50000 chr1 70000 + +
## #EAS139:136:FC706VJ:2:2342:15343:9863 chr1 60000 chr2 10000 + +
## #EAS139:136:FC706VJ:2:1286:25:275154 chr1 30000 chr3 40000 + -
##