Splicing doesn't appear to be handled correctly?

[choosehappy]

I have a BAM file which looks like this in IGV:

Note the splicing

plotting the same with pileup.js looks like this:

What is interesting is if i click on a location, this is the readout:

Which means i suspect that when pileup.js encounters an "N" in the cigar string, it simply adds a count to the last item in the bin.

I can't readily see where to correct that, but ifyou could point me in the right direction, i'd be happy to take a stab at correcting

thoughts?

[akmorrow13]

Thanks for finding this @choosehappy!

What is the expected output you intend to see in the popup? I believe the code you are looking for can be found in the getOpInfo function, which parses the cigar string. Is this what you are looking for?

We would love any contributions! The best way to get started would be to make a unit test in pileup utils , simulate a Alignment with a similar CigarString, and then test the modified getOpInfo function.

[choosehappy]

this is an example of one of the reads:

OBIWAN:364:CBYHYANXX:6:1103:3120:61918/1        0       integrated      108     60      115M8933N5M1S   *       0       0       GTTAGATATTTATTGATTTTTGGATGGTGTTATAAGTTAGTATTAGTTGAGTTAGATAAGGGAGAAGAGGTTAATAAAGGAGAGAATATAAGTTTGTTATATTTTGTGAGTTTGTATGGAG       FBFB7/F<FFFFFF<FF</F</B/<//F</<<<FBFBF<BBFFB<BF<B<B</FF</F<F<///<FB//F<////FF<FBBF/FB<<///B/FF<BFFBF<FF<///</FFFFFF</BBBB
       AS:i:-7 NM:i:2  MD:Z:61T27T30   NH:i:1  HI:i:1  YG:Z:C2T        YR:Z:C2T

The main point is to look at the cigar string:

115M8933N5M1S

It looks like the "8933N" is counted as a coverage, when in fact it should not be

I can verify this by looking at the pile up:

 samtools view -h 36_LV_sorted_1kreduced.bam integrated | samtools mpileup - > pileup.txt

looking at that particular location shown above:

 cat pileup.txt | grep 4322 | cut -f 5

this is what the bases look like:

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>A>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>AAA$AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

which coincides with these counts:

cat pileup.txt | grep 4322 | cut -f 5 | sed 's/\(.\)/\1\n/g' | sort | uniq -ic
   4263 >
      1 $
    909 A
      1 G

so, i would expect the pileup.js pop up to say:

909 A
1 G

While in fact all of the ">" are being bundled into the "A"

Do you see what i'm saying?

[choosehappy]

By the way, this is the entire pileup line for that point:

integrated      4322    N       5173    >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>A>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>AAA$AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA BBBB/BB/B/BBBBBB/BBBBBBBBBBBBBB<<BBBBBBBBBBBBBB<BBBBBBBB/BBBBBBBBBBBBBFBBBFBBF<BBBBB/BFB/B<BBB<BBBFBBBB<B/BFFFF/F7F/FFFFFFFFFFFFBFFFFFFFB<B/B//FB</BBBBBFFFBFFBFFBBFFFFFFFFFFFFFFFFFFBF/FFFFFBBB<BBFB/FBBFFFFFFB/FFFFFFFF<BBB<B<</</<<B<<</<FB<BBB<</BBBFBB</BB<<//B<BB/B/FF<B//F<BBFFBBB/BBFB<B<BB/<B<BBB<BF<<<B<B<<<<<//BB<<<<<</<<<</<<<<B/<<<</<B<</<F<B<<B</<BB<<<//</<<B<<<</<<<<<<B<B<<<<<<<<<B<<<<<BB<<<<<<<<<<B<B<B<B/<<<<B<<<<<<<B/<<<B<<<<<B/<</<<<<<<</<<<</<<<<<<<</</<B<<<<<<B<<<<<<<<<B<<BB</B<<<BBBB/BFF<FB<BBB<B<</BF</<B<<B<<<B<<<<<<<BB</<BBB/<F/<BBBBB/BB<<BBBFBB<B<B<</B<B<<B<<B<<<<<</B<<FBBBF<FBB<<B<<<B<F/B<BF<FB<<<B<<BBB<<<<BBBBF<BF/BBFFFFFFFFFFFFFFBBFFFFFFFBFFF<FFFFFFFFFFFFFFFFFFFFFF<FFBFFFFFFFFBFFFFFFFFBFFFFFFFFFFFFFFFFFFBFFFFFBFFFFFFBF/FFFFFFFFFFFFFFF<FFFFFFFFFFFFFBF<FFFFF/B<BB<//<<</<BBB<//<<FBBBBBBBBBBBBBBBBBBBBBBB//<FF/<BBBFF/F</BFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFF<B<<<<<B<<<<<F<<<BBB<<<B/</<FF////F/BBFFBB</<<BBFBBFF/FB<FBBB<BB</FB<FF/FFFF<BFFFBFFF/FFFF7FFFF</FF/F<BBFBBFB/BBBB/FFFFFFFB<FFFFFF//FF<FBF<BBBF<F<<BBB//BBF/<BFBFFFFFB<<<<FFBBFFB</B<BFBBBB<///FBF<FBFBB</<F<<BBBFBFF<FFFFB<F/F/BBB<</<<BB<</BF<B/B/<FFFFBB//FBFBFB<F/FBBB</BF/<//<<BB<FBF</<BBFB/FFBBFBB<FFF//BFBFFFF/<<FBF/F/</B<<<<<BB</FB/<FBFF//F<F</B//<BFFFFFB/FFBB/FFFFFFFFB/BF/FFFFFF/<FF/FBBFBFFF<FFFB/<BBF/F<B<BF/<</B/BFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFBFF/F/FFFFFBFFFFF<FFFFFFFB<<B</FFFFFF<FFFFFFFBFFFFFFF7FFFFFFF<FFF/FFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFBFFFFFFF<FFFFFFFFFFFFFFFFFFBBFFFFFFFFFF/FFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFF/F<BBFFFB/FBBFF/BF</<<B<B/B<B/<F<//B//</<B<FFBBFB<BB<FFF/<//FB<<//B//<B</<FFFF<F<FBFBBBBF///FF<BB<BF<<B/F/<BF<<F<B<</BBFBB/BBBF<<FFFFFFFFFBBF</FB/BF/B/F/B<F</BFFFFFFF/FFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<FFFF/FFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFBFFFFFFFFFF<FFFFFFFFFFFFF/FFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF/BFFFFFFFFFFFFFF/FFBFFFFFFFBFB/BFFFFF//F//FFFFFFF<FFF<7F<F<FBFFFF/FBFB<BBBBBBBBBBBB<<B<<B/B/BBB<<BBB/<B<BBBBBBBBBBBBBBBBBB<BBBB<BBBB/BBBBBBBBBB<BBB<BBBBBBB<BBBB<BBB/<</B<//B<BFF/B//BBB/B/BB<<BBBB<<BBBB/BB<BBBB<BBB/BBBBBBBFBBBBB/B/<BBBB<FFFFFFFFFFFFFFFFFBFFFFFFFFFFF/FFFFFFFBFFFFFFFFFFFB/<<F/FBFFFFFFFFFFBFF/<FFFFFF/FFFF/BBBB/B/FFBBFB/BB/BBBBBB/BBBBBFBB<<B//B/BBFBF<BBBBBBB<B<FB<FBB<BFB<BB/<<B/BBBB<B<BBBB<<BBFBFBBBB/</BBB/<FBBBBBBBBBBBBBB/BBBF/BBB/<BB/B/B//BFBB/<<FBBBFBBB<BBBBBBBB//<BFBBBFBBBB<BBF<<B</BBBBBFB<BB<BBBB/BB<<B<BBBB<B</</BBBB<BBBBBBBB<BBB<BBBB//BBBBBFBBBB<<BBBBFBB/BB<B<<BBBBBBBB<BFBBBB<<BBBBF/FBBB<B<BBBB<F/BB</B</<<B/BB</FBB/BBBBBFB<///FB<B/BF/B/BBFBBF<BFFB//<FFBBBBBBBBBBBBBBBBBBBBBBBBFBBB<BBBBBBFFFFFB<<BBFBBBB/B<B/BFBFFBFFB</FFBBB<B</FFFFFFFFFF<BBB</BBFF/B<B<<BBFFFBBFFFBFBFBB<FBFBBBBBBBFBBB/BFBB/B/BBFBFFFBFFFFFBFFFFFFFFF/FFFFBFFFFFFBFFBF<BBBFBBBBBBFBB/BBBBBBBBBBBFBBBB<BFFFFFFBFFBFFFFBFFFFFFFFF<BFBBBBBBBBB/FFFB<BFFFBFFFFBFFBBFFFFFBFFFF/BFFFFBBFFB<FFFFBFFFFFFFFFFFBFBBBFBBBBBFFFFBBFBBB/BBBBBBBBBBBBBBBBBBBBBBBBBBBBBFFFBBB/BBBBBBBB<BBBBBBFF<<FFFBBBB<BF/BBBBBBB/<FFFFFBFFFFFFFFFFFFFFFFFFFFBFBBFBBF/B<//B<</B//</<///F<<BBBBF<</<B<FBFB/FB/B<//FB///BF<FF/BF/FB/FB/FFBF//F</<FF<//BFFBF<</FBF/F<B///F<FF/FF//F<////</BFF//<<<<B<</B<F/F//<FFF<FFB/F<<FF/</FBFFB<<//BB/F<<</FFF<//B/<FB<F/</<<F</FF/FF/F<FFFFFFF/F<BFFFBFF/F<///B<BFFF/FF</<FF<F<F<B//F<<F<BBF<FF<BFB</F<<F/F/FFF<FFBF<FFFF/FF/FFF<FFFFFBFFFFFFFFFF<FFFBFFFFFFFFFFFFF<F<BF7FFFFFF<BFFFFFFF<FFFF<FBFB<F<FBF7FFFFFFFFFFB/FFFFFFFFFFFF7<FFFFFF<FFFB7FFF/FFFF7BFBFFFFFFFF/<BFFFFFF<F<FFF/FFFFFFFFFFFF/<FFF//FFFFBFFFF7FBFF<FFFFFFFFFFFFFFFFFFFBBB/FFFFB/FFFFFFFF7FFFBFFFFF<FFFFF<FFFBFBFFFFFFFFFFFFFF/BBBBBBBFFFFFBBBFFFFF/FFF/BBFFFF/FFFB<<<B<<<</<<//B<<</BB<<B<BB<BBFBBBFB<<B<B/<//B/B<BB<</B<B/<B<</B<B<F<<B<<</<F/<B<<BFFFFBBBBF/BBBBFFBFFFFFFFF//FBF<F/FF/FFB<BB<FF/FBFBFFFFBFFFBFF</<FB<<<BBB/<BBBBBB<BBB<BB/<FFFFFFFFBBFBBFFBFFFFFFFFFFFBBFF<FF/FBFFFFFFFFBFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFB/BBBBBBBBBBBB//////////B//BBFBFFFFFFFFFF/F/FFFFFFFFFBBBFF/FFFFBF/F/F/<B<B/FBFF<F</FBFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFF<FFFFFFFFF<FFFFFBFFFFFF/FFFFFFFFFBFFFFFFFF/FFF/<///FB<BBFFBBBF//FBB<BBB<BB<<BB</F/F/B/</<BBBBFFB<FBBBFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFFFFFFFFFBFFFFFFFFFFFFFF<FFBFFFFFFFFBFFFFFFB<FFFFF<FBFFFFFFFF<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFF/FFFFFFFFFFFFFFFFFFFBFFFFFFFF/FF/<FFFFFF/FFF/FFFFFFFFFFFFFFFFFFFF<F/FFFFFFFFFFFFFFFFFFFFFFFF<FFFF<FFFFFFFFFFFFFFFFFBFFFF/FFFFF<FFFFFFFFFFFFFBFFFFFF<F<FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFF/FFFFFFFFFFFF<FFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFF<FFFF/FFFFFFFFFFF/FFFFFFFFFFFFFFFFFBFFBFFBFFFFFFFFFFFFFFFFFFFFFFFF<FFFFFFF/FF/FFFFFFBFFFFFFFFF<FFFFFF/FFFFFFBFFFFFFFFFFFFF<FFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFF<FFFFFFFFFFF/FFFFFFFBFFFFFFFFFFFFFFFFFFFF<FFFFFFFFFFFFBFFFFFFFFF<FFFFFBFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF/FF/FFFFFFFFFFFFFFB/FFFFFFFFFFFFFFFFBBFFBBFFFF<FF<FFFFFFFFFFFFFFF

so pileup.js is reporting the coverage is "5173 " when really it should be 910, with 909 being "A" and "1" being G