added samtools flagstat only mapped

phages/steps/mapping/README.md

+Mapping statistics:
+
+Percentage andnumber of reads mapped per sample in file `mapping_flagstat.txt`, created like this
+```bash
+cd mapping
+for i in $(find . -name *.bam); 
+do 
+    echo -ne $i'\t'$(samtools flagstat -@ 10 $i | grep 'mapped (')'\n'  >> mapping_flagstat.txt; 
+done
+```
\ No newline at end of file

phages/steps/mapping/mapping_flagstat.txt

+./R_seq/R4T1_S30.sort.bam	266703 + 0 mapped (96.62% : N/A)
+./R_seq/R1T2_S43.sort.bam	201728 + 0 mapped (98.19% : N/A)
+./R_seq/R6T4_S80.sort.bam	283192 + 0 mapped (98.22% : N/A)
+./R_seq/R8T1_S34.sort.bam	193210 + 0 mapped (98.45% : N/A)
+./R_seq/R1T1_S27.sort.bam	267129 + 0 mapped (93.48% : N/A)
+./R_seq/R6T2_S48.sort.bam	276422 + 0 mapped (98.15% : N/A)
+./R_seq/R3T4_S77.sort.bam	215943 + 0 mapped (98.77% : N/A)
+./R_seq/R7R3_S65.sort.bam	238639 + 0 mapped (98.41% : N/A)
+./R_seq/R5T3_S63.sort.bam	219309 + 0 mapped (98.59% : N/A)
+./R_seq/R3T2_S45.sort.bam	188361 + 0 mapped (98.72% : N/A)
+./R_seq/R7R2_S49.sort.bam	340393 + 0 mapped (97.47% : N/A)
+./R_seq/R2T1_S28.sort.bam	331082 + 0 mapped (93.65% : N/A)
+./R_seq/R8T4_S82.sort.bam	159514 + 0 mapped (90.90% : N/A)
+./R_seq/R6T1_S32.sort.bam	280938 + 0 mapped (96.06% : N/A)
+./R_seq/R7R1_S33.sort.bam	142124 + 0 mapped (98.93% : N/A)
+./R_seq/R5T4_S79.sort.bam	628414 + 0 mapped (98.62% : N/A)
+./R_seq/R8T2_S50.sort.bam	210701 + 0 mapped (97.89% : N/A)
+./R_seq/R2T3_S60.sort.bam	256842 + 0 mapped (98.28% : N/A)
+./R_seq/R4T4_S78.sort.bam	234475 + 0 mapped (98.31% : N/A)
+./R_seq/R2T4_S76.sort.bam	212134 + 0 mapped (98.56% : N/A)
+./R_seq/R3T3_S61.sort.bam	321965 + 0 mapped (98.75% : N/A)
+./R_seq/R3T1_S29.sort.bam	353462 + 0 mapped (95.05% : N/A)
+./R_seq/R7T2-B_S89.sort.bam	109270 + 0 mapped (97.39% : N/A)
+./R_seq/R4T3_S62.sort.bam	215337 + 0 mapped (96.72% : N/A)
+./R_seq/R4T2_S46.sort.bam	282404 + 0 mapped (93.47% : N/A)
+./R_seq/R5T1_S31.sort.bam	342830 + 0 mapped (96.21% : N/A)
+./R_seq/R7R4_S81.sort.bam	138458 + 0 mapped (98.62% : N/A)
+./R_seq/R2T2_S44.sort.bam	199842 + 0 mapped (97.71% : N/A)
+./R_seq/R5T2_S47.sort.bam	130208 + 0 mapped (98.66% : N/A)
+./R_seq/R1T3_S59.sort.bam	108547 + 0 mapped (98.84% : N/A)
+./R_seq/R8T3_S66.sort.bam	314123 + 0 mapped (98.71% : N/A)
+./R_seq/R4T2-B_S88.sort.bam	4507 + 0 mapped (86.01% : N/A)
+./R_seq/R6T3_S64.sort.bam	327952 + 0 mapped (98.32% : N/A)
+./R_seq/R1T4_S75.sort.bam	270293 + 0 mapped (98.21% : N/A)
+./Other_seq/C4-B_S15.sort.bam	333006 + 0 mapped (98.83% : N/A)
+./Other_seq/C6-C_S6.sort.bam	22 + 0 mapped (91.67% : N/A)
+./Other_seq/C7-A_S5.sort.bam	222530 + 0 mapped (98.30% : N/A)
+./Other_seq/A8-C_S12.sort.bam	175975 + 0 mapped (99.25% : N/A)
+./Other_seq/Undetermined_S0.sort.bam	258272 + 0 mapped (28.70% : N/A)
+./Other_seq/2972_S17.sort.bam	490667 + 0 mapped (98.62% : N/A)
+./Other_seq/B8-B_S14.sort.bam	251670 + 0 mapped (98.78% : N/A)
+./Other_seq/D5-A_S1.sort.bam	123792 + 0 mapped (98.81% : N/A)
+./Other_seq/C3-E_S7.sort.bam	200148 + 0 mapped (97.96% : N/A)
+./Other_seq/D1-D_S3.sort.bam	127587 + 0 mapped (98.42% : N/A)
+./Other_seq/B9-B_S10.sort.bam	169169 + 0 mapped (98.69% : N/A)
+./Other_seq/TO-MIX_S84.sort.bam	264450 + 0 mapped (89.05% : N/A)
+./Other_seq/B7-A_S9.sort.bam	170581 + 0 mapped (98.60% : N/A)
+./Other_seq/CTRL2_S96.sort.bam	12 + 0 mapped (25.00% : N/A)
+./Other_seq/TO-WT_S83.sort.bam	238738 + 0 mapped (96.64% : N/A)
+./Other_seq/CTRL1_S25.sort.bam	166 + 0 mapped (96.51% : N/A)
+./Other_seq/T4-B_S93.sort.bam	165247 + 0 mapped (98.85% : N/A)
+./Other_seq/C8-A_S2.sort.bam	178065 + 0 mapped (98.65% : N/A)
+./Other_seq/A10-A_S16.sort.bam	407134 + 0 mapped (98.42% : N/A)
+./Other_seq/A7-A_S8.sort.bam	232892 + 0 mapped (98.62% : N/A)
+./Other_seq/D6-B_S4.sort.bam	236362 + 0 mapped (98.55% : N/A)
+./Other_seq/A9-A_S13.sort.bam	606878 + 0 mapped (97.69% : N/A)
+./Other_seq/C2-B_S11.sort.bam	341594 + 0 mapped (98.75% : N/A)
+./W_seq/W3T1-bis_S95.sort.bam	91294 + 0 mapped (98.45% : N/A)
+./W_seq/W3T2_S37.sort.bam	240683 + 0 mapped (95.44% : N/A)
+./W_seq/W5T3_S55.sort.bam	242348 + 0 mapped (98.63% : N/A)
+./W_seq/W8T4-B_S92.sort.bam	182827 + 0 mapped (98.39% : N/A)
+./W_seq/W5T1_S22.sort.bam	82301 + 0 mapped (98.28% : N/A)
+./W_seq/W8T2_S42.sort.bam	1853492 + 0 mapped (97.16% : N/A)
+./W_seq/W8T3_S58.sort.bam	319089 + 0 mapped (98.50% : N/A)
+./W_seq/W2T2-B_S85.sort.bam	66261 + 0 mapped (95.27% : N/A)
+./W_seq/W7T3_S57.sort.bam	395765 + 0 mapped (98.80% : N/A)
+./W_seq/W8T1_S26.sort.bam	271019 + 0 mapped (98.66% : N/A)
+./W_seq/W8T4_S74.sort.bam	97472 + 0 mapped (90.43% : N/A)
+./W_seq/W7T2_S41.sort.bam	161632 + 0 mapped (97.57% : N/A)
+./W_seq/W7T4-B_S91.sort.bam	4797 + 0 mapped (84.60% : N/A)
+./W_seq/W1T2_S35.sort.bam	112966 + 0 mapped (94.31% : N/A)
+./W_seq/W6T4_S72.sort.bam	286616 + 0 mapped (96.76% : N/A)
+./W_seq/W4T1_S21.sort.bam	157715 + 0 mapped (73.88% : N/A)
+./W_seq/W4T2_S38.sort.bam	275784 + 0 mapped (80.20% : N/A)
+./W_seq/W7T4_S73.sort.bam	112917 + 0 mapped (87.71% : N/A)
+./W_seq/W5T2-B_S87.sort.bam	11830 + 0 mapped (87.80% : N/A)
+./W_seq/W2T1_S19.sort.bam	407436 + 0 mapped (98.04% : N/A)
+./W_seq/W3T4_S69.sort.bam	116257 + 0 mapped (57.62% : N/A)
+./W_seq/W2T2_S36.sort.bam	280465 + 0 mapped (91.45% : N/A)
+./W_seq/W2T4_S68.sort.bam	263439 + 0 mapped (98.80% : N/A)
+./W_seq/W1T4_S67.sort.bam	674210 + 0 mapped (98.60% : N/A)
+./W_seq/W6T2_S40.sort.bam	230775 + 0 mapped (97.91% : N/A)
+./W_seq/W4T3_S54.sort.bam	135301 + 0 mapped (98.53% : N/A)
+./W_seq/W5T2_S39.sort.bam	181659 + 0 mapped (84.31% : N/A)
+./W_seq/W3T1_S20.sort.bam	134076 + 0 mapped (98.23% : N/A)
+./W_seq/W6T1_S23.sort.bam	97327 + 0 mapped (98.18% : N/A)
+./W_seq/W1T3_S51.sort.bam	240111 + 0 mapped (98.56% : N/A)
+./W_seq/W4T4_S70.sort.bam	254685 + 0 mapped (98.60% : N/A)
+./W_seq/W6T3_S56.sort.bam	625915 + 0 mapped (98.93% : N/A)
+./W_seq/W7T1_S24.sort.bam	176338 + 0 mapped (98.33% : N/A)
+./W_seq/W3T3_S53.sort.bam	280516 + 0 mapped (97.40% : N/A)
+./W_seq/W3T4-B_S90.sort.bam	7906 + 0 mapped (84.76% : N/A)
+./W_seq/W7T1-B_S94.sort.bam	156866 + 0 mapped (99.39% : N/A)
+./W_seq/W2T3_S52.sort.bam	76540 + 0 mapped (95.87% : N/A)
+./W_seq/W5T4_S71.sort.bam	214734 + 0 mapped (98.92% : N/A)
+./W_seq/W1T1_S18.sort.bam	332421 + 0 mapped (97.72% : N/A)
+./W_seq/W4T2-B_S86.sort.bam	25686 + 0 mapped (85.24% : N/A)