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#70 make isize 0 when reads map to different ref sequences.

open
bowtie (72)
5
2014-08-21
2012-02-23
Anonymous
No

In the samtools output field, there are non-0 insert sizes for reads that map to different reference sequences. It would be really nice for quick scripts checking insert size distributions if these values were set to 0 like they are in bwa. Thanks for your time!

* 65 scaffold-20138 298160 0 55M2I33M scaffold-17396 120 -298040 NAAAGTGGGCTCAGCACAGCCGGCTGCCGCCTCCTTCCTCAGGGTCCCTGGTCCCGCCAGGAGCGTGTCGAAGGTGCCCAGCTGCAGACT !*.)').)*+@@@@@@@@@@@@@@@17757<:<<<@@@:@)----:::::87999@@22@!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
* 129 scaffold-17396 120 0 57M1D33M scaffold-20138 298160 298040 TCAGGCAGGGGAGAGAAAGTGAAACCCTCCAAAGTGGGGCCGTGACCTCCTGAAACCCCCCCTGCTCACCGGTGTCTGCGAGGCTGAGCT HIGIHIIIDHEBI7EGGDEGGGGGGI@@HDAFEDAGGG@D8ED<<GGEGE2EB<BGGGGGGD;<<8?=?=C>.??@<8=?>A>A!!!!!!
* 113 scaffold-22045 1961 18 90M scaffold-10988 1788 -173 CAATCATAGTGCACAACAGTCCTCTCACCCCATGAATGCCAAGATGTTTATTTGCTGCTTTTATAAGAAATGACTGCACAGCCACGGTTN @@;@@CC@@@@;@@@@@C@@@@@@22@@@@@@CCC@CC@@CC@@@222@@C@@C@C@22CCC@22C@@@@@C@@@@@@@@55566....!
* 177 scaffold-10988 1788 18 90M scaffold-22045 1961 173 TGTGGCTGGTCAGCACGAACCTCTCCCACCGCTGTCTGTCACTACATTGCACAGATAAGAAGGTGCGTAAGGGGCACCGCAGCTGTCCTG @??@A=:@@@?>>?7<?<?A<@8<CEEB@EICHIEEEEGEBG8CGHIFIIGIEIIHIIHGIIIIIHIIIHIIIIIHIIIHIIIIIIEIII

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